S. A. Ohnmacht et al. / Bioorg. Med. Chem. Lett. 22 (2012) 5930–5935
5935
14. Lim, K. W.; Lacroix, L.; Yue, D. J.; Lim, J. K.; Lim, J. M.; Phan, A. T. J. Am. Chem. Soc.
2010, 132, 12331.
(CH2), 53.2 (CH2), 46.1 (CH3), 33.6 (CH2). HRMS (ES+) calculated for C38H44N6O2
(M+H)+ 617.3604, found 617.3626. Mp 191–193 °C (pale-yellow solid).
15. Tong, X.; Lan, W.; Zhang, X.; Wu, H.; Liu, M.; Cao, C. Nucleic Acids Res. 2011, 39,
6753.
16. Neckers, L.; Workman, P. Clin. Cancer Res. 2012, 18, 64.
17. Millson, S. H.; Chua, C. S.; Roe, S. M.; Polier, S.; Solovieva, S.; Pearl, L. H.; Sim, T.
S.; Prodromou, C.; Piper, P. W. FASEB J. 2011, 25, 3828.
18. See for example: (a) Keppler, B. R.; Grady, A. T.; Jarstfer, M. B. J. Biol. Chem.
2006, 281, 19840; (b) Kim, R. H.; Kim, R.; Chen, W.; Hu, S.; Shin, K. H.; Park, N.
H.; Kang, M. K. Carcinogenesis 2008, 29, 2425.
19. Cogoi, S.; Xodo, L. E. Nucleic Acids Res. 2006, 34, 2536.
20. Capbell, N. H.; Parkinson, G. N.; Reszka, A. P.; Neidle, S. J. Am. Chem. Soc. 2008,
130, 6722.
21. See also Nielsen (a) Kim, M.-Y.; Vankayalapati, H.; Shin-ya, K.; Wierzba, K.;
Hurley, L. H. J. Am. Chem. Soc. 2002, 124, 2098; (b) Rzuczek, S. G.; Pilch, D. S.;
Liu, A.; Liu, L.; LaVoie, E. J.; Rice, J. E. J. Med. Chem. 2010, 53, 3632; (c) Ulven, M.
C. T. Curr. Med. Chem. 2010, 17, 3438. for a recent review of macrocyclic
quadruplex ligands..
28. FRET DNA melting assays on compounds 2a–k were performed as described
previously (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 to be used as a high-throughput screen in a 96-well format.
The labelled oligonucleotides had attached the donor fluorophore FAM:
6-carboxyfluorescein and the acceptor fluorophore TAMRA: 6-carboxytetram-
ethylrhodamine. The FRET probe sequences were diluted from stock to the
correct concentration (400 nM) in a 60 mM potassium 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 (eg. F21T). 96-Well plates
(MJ Research, Waltham, MA) were prepared by aliquoting 50
ll of the annealed
DNA into each well, followed by 50 of the compound solutions.
ll
22. (a) Moorhouse, A. D.; Santos, A. M.; Gunaratnam, M.; Moore, M.; Neidle, S.;
Moses, J. E. J. Am. Chem. Soc. 2006, 128, 15972; (b) Drewe, W. C.; Neidle, S.
Chem. Commun. 2008, 5295.
23. Reeder, M. R.; Gleaves, H. E.; Hoover, S. A.; Imbordino, H. R.; Pangborn, J. J. Org.
Process Res. Dev. 2003, 7, 696.
24. van Leusen, A. M.; Hoogenboom, B. E.; Siderius, H. Tetrahedron Lett. 1972, 23,
2369.
25. Strotman, N. A.; Chobanian, H. R.; Gou, Y.; He, J.; Wilson, J. E. Org. Lett. 2010, 16,
3578.
Measurements were made on a DNA 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 a script written in the
program Origin 7.0 (OriginLab Corp., Northampton, MA). The advanced curve-
fitting function in Origin 7.0 was used for calculation of
DTm are 0.1 °C.
DTm values. Esds in
29. Sulforhodamine B assay (SRB). Cells were counted and diluted to the required
concentration in 20 mL medium. For cell lines MCF7, A549, MIA-Pa-Ca-2, RCC4
26. Ohnmacht, S. A.; Mamone, P.; Culshaw, A. J.; Greaney, M. F. Chem. Commun.
2008, 10, 1241.
and 786-0, 1000–4000 cells with 160
into each well of a 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
lL media (WI38: 6000/well) were seeded
27. Synthesis and analytical data for compound 2f, 1,3-bis(2-(4-(2-(4-
methylpiperazine-1-yl)ethyl)phenyl)-oxazol-5-yl)benzene. A 5 mL microwave
vial was charged with phenyl bis-oxazole (40 mg, 0.19 mmol, 1 equiv), 4-(4-
iodobenzyl)-4-methylpiperazine (120 mg, 0.4 mmol, 2.1 equiv), Pd(dppf)Cl2ꢀ-
CH2Cl2 (16 mg, 0.019 mmol, 10 mol%), Ag2CO3 (105 mg, 0.38 mmol, 2 equiv)
and PPh3 (10 mg, 0.038 mmol, 20 mol %). A magnetic stirrer bar was added and
the mixture of solids was gently shaken for a few seconds to ensure all solids
were well mixed. Distilled water (3 mL) was added and the vial was covered
with a serum cap. The vial and its contents were then heated and stirred in a
pre-heated oil bath at 60 °C for 36 h. After this time the reaction mixture was
cooled down to room temperature. CH2Cl2 (4 ml) was added and the contents
of the vial were filtered through a short pad of celite (in a Pasteur pipette with
cotton wool at bottom). The vial was rinsed once with an additional 1 ml of
CH2Cl2. The organic layer was separated, and the aqueous phase extracted once
with CH2Cl2 (1 ml). The organic layers were combined and concentrated in
l
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 5 times and dried at 60 °C for 1 h. The cells were then
incubated with sulforhodamine
Organics, 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,
B (80 lL, 0.4 % in 1% acetic acid, Acros
l
l
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%.
vacuo. The residue was purified by flash chromatography (silica; CH2Cl2
/
MeOH 9:1) to provide the title compound as an off-white solid in 78% yield.
Best purification results were obtained when a gradient from CH2Cl2 (100%) to
CH2Cl2 : MeOH (7:3) was applied. 1H NMR (400 MHz, CDCl3) d 8.06 (4H, d,
J = 8 Hz, Ar-H), 8.00 (1H, s, Ar-H), 7.68 (2H, dd, J = 8 Hz, 8 Hz, Ar-H), 7.54–7.50
(3H, m, Ar-H), 7.35 (4H, d, J = 8 Hz, Ar-H), 2.91–2.87 (4H, m, 2 ꢁ CH2), 2.68–
2.50 (20H, m, 10 ꢁ CH2), 2.31 (6H, s, 2 ꢁ CH3). 13C NMR (100 MHz, CDCl3) d
161.7 (quat), 150.5 (quat), 143.4 (quat), 129.6 (quat), 129.3 (CH), 128.9 (CH),
126.5 (CH), 125.3 (CH), 124.2 (CH), 124.0 (CH), 119.6 (quat), 60.0 (CH2), 55.2
30. Gunaratnam, M.; de la Fuente, M.; Hampel, S. M.; Todd, A. K.; Reszka, A. P.;
Schatzlein, A.; Neidle, S. Bioorg. Med. Chem. 2011, 19, 7151.
31. Hamon, F.; Large, E.; Guédin-Beaurepaire, A.; Rouchon-Dagois, M.; Sidibe, A.;
Monchaud, D.; Mergny, J.-L.; Riou, J.-F.; Nyugen, C.-H.; Teulade-Fichou, M.-P.
Angew. Chem., Int. Ed. 2011, 50, 8745.
32. Collie, G. W.; Promontorio, R.; Hampel, S. M.; Micco, M.; Neidle, S.; Parkinson,
G. N. J. Am. Chem. Soc. 2012, 134, 2723.
33. Dai, J.; Carver, M.; Hurley, L. H.; Yang, D. J. Am. Chem. Soc. 2012, 134, 17673.