Y.-L. Chen et al. / Bioorg. Med. Chem. 20 (2012) 4790–4800
4799
Pike, R.; Ruan, S.; Santhanam, B.; Vibulbhan, B.; Wu, W.; Yang, W.; Kong, J.;
Liang, X.; Wong, J.; Liu, R.; Butkiewicz, N.; Chase, R.; Hart, A.; Agrawal, S.;
Ingravallo, P.; Pichardo, J.; Kong, R.; Baroudy, B.; Malcolm, B.; Guo, Z.; Prongay,
A.; Madison, V.; Broske, L.; Cui, X.; Cheng, K.-C.; Hsieh, T. Y.; Brisson, J.-M.;
Prelusky, D.; Korfmacher, W.; White, R.; Bogdanowich-Knipp, S.; Pavlovsky, A.;
Bradley, P.; Saksena, A. K.; Ganguly, A.; Piwinski, J.; Girijavallabhan, V.;
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Biosystems, catalog number 402869). The samples were analyzed
in triplicate per experiment and the experiment performed two
independent times. Samples were processed using a Mastercycler
ep realplex2 gradient S (Eppendorf) with cycling parameters of
50 °C for 2 min, 95 °C for ten min, 95 °C for 15 s, 60 °C for 1 min, re-
peat latter two steps 39 more times. Parallel wells of lysate were
analyzed for either HCV replicon RNA or GAPDH RNA and relative
levels of HCV RNA calculated using the comparative method.53 The
PCR efficiency for the two sets of primers/probe was determined
using 5-fold serial dilutions (over 3logs) of lysate from replicon
cells as described53 and was 100% (R2 0.999) and 110% (R2 0.997)
for NS5B primers/probe and GAPDH primers/probe, respectively.
16. Arasappan, A.; Bennett, F.; Bogen, S. L.; Venkatraman, S.; Blackman, M.; Chen,
K. X.; Hendrata, S.; Huang, Y.; Huelgas, R. M.; Nair, L.; Padilla, A. I.; Pan, W.;
Pike, R.; Pinto, P.; Ruan, S.; Sannigrahi, M.; Velazquez, F.; Vibulbhan, B.; Wu,
W.; Yang, M.; Saksena, A. K.; Girijavallabhan, V.; Shih, N.-Y.; Kong, J.; Meng, T.;
Jin, Y.; Wong, J.; McNamara, P.; Prongay, A.; Madison, V.; Piwinski, J. J.; Cheng,
K.-C.; Morrison, R.; Malcolm, B.; Tong, X.; Ralston, R.; Njoroge, F. G. ACS Med.
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Girijavallabhan, V.; Tong, X.; Cheng, K.-C.; Njoroge, F. G. J. Med. Chem. 2009, 52,
2806.
18. Bennett, F.; Huang, Y.; Hendrata, S.; Lovey, R.; Bogen, S. L.; Pan, W.; Guo, Z.;
Prongay, A.; Chen, K. X.; Arasappan, A.; Venkatraman, S.; Velazquez, F.; Nair, L.;
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Saksena, A. K.; Njoroge, F. G. Bioorg. Med. Chem. Lett. 2010, 20, 2617.
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Njoroge, F. Bioorg. Med. Chem. 1854, 2010, 18.
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1370.
4.3.5. HCV NS5B assay
Primer-dependent NS5B
using a scintillation proximity assay (SPA) as described.44 Briefly,
purified NS5B 55 (2 nM) was added to Mix 1 (20 mM Tris pH
7.5, 50 mM NaCl, 5 mM KCl, 0.5 mM MnCl2, 4U RNasin (Promega),
1 mM DTT, 1 L compound in DMSO or 1 L DMSO alone) and Mix
2 was added (450tnM Oligo-U12 primer, 30 nM UTP, 75 nM
Poly(A) template, 0.2 L reaction was incu-
i [3H]UTP). The 41
bated in 0.7 mL tubes at room temperature for 3 h and stopped
by adding 350 L of 1.2 mg streptavidin-coated SPA beads (Perkin-
D55 polymerase activity was measured
D
l
l
l
l
21. Nair, L. G.; Bogen, S.; Ruan, S.; Pan, W.; Pike, R.; Tong, X.; Cheng, K.-C.; Guo, Z.;
Doll, R. J.; Njoroge, F. G. Bioorg. Med. Chem. Lett. 2010, 20, 1689.
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24. Liu, Y.; He, Y.; Molla, A. Antiviral Res. 2009, 137.
l
Elmer) in 0.15 M EDTA. The samples were analyzed immediately
for 1 min in a scintillation counter. Each compound concentration
was performed in duplicate and repeated at least two independent
times. (see Scheme 1)
25. Beaulieu, P. L. Curr. Opin. Invest. Drugs 2007, 8, 614.
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Acknowledgements
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This research was supported by the Center for Drug Design at
the University of Minnesota. We thank Dr. Guangxiang Luo at Uni-
versity of Kentucky for providing the Huh-7/HCV1b-Rluc replicon
cells and Matthew Kesler for technical assistance.
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Supplementary data
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