7094
R. Romagnoli et al. / Bioorg. Med. Chem. 20 (2012) 7083–7094
performed using plants.33 Molecular dynamics was performed
with the Gromacs 4.534 with the Amber99 force field. The structure
was solvated using TIP3P water molecules, providing a minimum
of 9.0 Å of water between the protein surface and any periodic
box edge. The system was neutralized, minimized and then a posi-
tion restrain dynamics simulation was carried out for 150 ps. The
production simulation was conducted for 2 ns at 298 K using a
NPT environment. Inhibitors were parameterized by Antechamber
of AmberTool 1.5.35 Trajectories analysis were carried out by
VMD.35
Supplementary data
Supplementary data associated with this article can be found, in
References and notes
1. (a) Honore, S.; Pasquier, E.; Braguer, D. Cell. Mol. Life Sci. 2005, 62, 3039; (b)
Amos, L. A. Org. Biomol. Chem. 2004, 2, 2153.
2. (a) Dumontet, C.; Jordan, M. A. Nat. Rev. Drug Disc. 2010, 9, 790; (b) Risinger, A.
L.; Giles, F. J.; Mooberry, S. L. Cancer Treat. Rev. 2008, 35, 255; (c) Hearn, B. R.;
Shaw, S. J.; Myles, D. C. Compr. Med. Chem. II 2007, 7, 81.
3. (a) Yue, Q.-X.; Liu, X; Guo, D.-A. Planta Med. 2010, 76, 1037; (b) Kingston, D. G. J.
Nat. Prod. 2009, 72, 507.
4. Pettit, G. R.; Singh, S. B.; Hamel, E.; Lin, C. M.; Alberts, D. S.; Garcia-Kendall, D.
Experentia 1989, 45, 209.
5. Lin, C. M.; Ho, H. H.; Pettit, G. R.; Hamel, E. Biochemistry 1989, 28, 6984.
6. McGown, A. T.; Fox, B. W. Cancer Chemother. Pharmacol. 1990, 26, 79.
7. Pettit, G. R.; Temple, C., Jr.; Narayanan, V. L.; Varma, R.; Boyd, M. R.; Rener, G.
A.; Bansal, N. Anti-Cancer Drug Des. 1995, 10, 299.
8. (a) Rustin, G. J.; Shreeves, G.; Nathan, P. D.; Gaya, A.; Ganesan, T. S.; Wang, D.;
Boxall, J.; Poupard, L.; Chaplin, D. J.; Stratford, M. R. L.; Balkissoon, J.; Zweifel, M.
Br. J. Cancer 2010, 102, 1355; (b) Siemann, D. W.; Chaplin, D. J.; Walike, P. A.
Expert Opin. Investig Drugs 2009, 18, 189.
9. Tron, G. C.; Pirali, T.; Sorba, G.; Pagliai, F.; Busacca, S.; Genazzani, A. A. J. Med.
Chem. 2006, 49, 3033.
5.9.4. Flow cytometric analysis of cell cycle distribution
For flow cytometric analysis of DNA content, 5 ꢂ 105 HeLa or
Jurkat cells in exponential growth were treated with different con-
centrations of the test compounds for 24 or 48 h. After incubation,
the cells were collected, centrifuged and fixed with ice-cold ethanol
(70%). The cells were treated with lysis buffer containing RNAse A
and 0.1% Triton X-100 and stained with PI. Samples were analyzed
on a Cytomic FC500 flow cytometer (Beckman Coulter). DNA histo-
grams were analyzed using MultiCycleÒ for Windows (Phoenix
Flow Systems).
10. (a) Nam, N. H. Curr. Med. Chem. 2003, 10, 1697; (b) Cushman, M.; Nagarathnam,
D.; Gopal, D.; He, H.-M.; Lin, C. M.; Hamel, E. J. Med. Chem. 1992, 35, 2293; (c)
Hatanaka, T.; Fujita, K.; Ohsumi, K.; Nakagawa, R.; Fukuda, Y.; Nihei, Y.; Suga,
Y.; Akiyama, Y.; Tsuji, T. Bioorg. Med. Chem. Lett. 1998, 8, 3371.
11. (a) Chaudari, A.; Pandeya, S. N.; Kumar, P.; Sharma, P. P.; Gupta, S.; Soni, N.;
Verma, K. K.; Bhardwaj, G. Mini-Rev. Med. Chem. 2007, 12, 1186; (b) Hsieh, H. P.;
Liou, J. P.; Mahindroo, N. Curr. Pharm. Des. 2005, 11, 1655.
12. Romagnoli, R.; Baraldi, P. G.; Brancale, A.; Ricci, A.; Hamel, E.; Bortolozzi, R.;
Basso, G.; Viola, G. J. Med. Chem. 2011, 54, 5144.
5.9.5. Annexin-V assay
Surface exposure of PS on apoptotic cells was measured by flow
cytometry with a Coulter Cytomics FC500 (Beckman Coulter) by
adding annexin-V-FITC to cells according to the manufacturer’s
instructions (Annexin-V Fluos, Roche Diagnostic). Simultaneously,
the cells were stained with PI.
13. Brown, M. D.; Gillon, D. W.; Meakins, G. D.; Whitham, G. H. J. Chem. Soc., Perkin.
Trans. I 1985, 1623.
14. Dall’Acqua, F.; Linardi, M. A.; Maggi, F.; Nicoletti, M.; Petitto, V.; Innocenti, G.;
Basso, G.; Viola, G. Bioorg. Med. Chem. 2011, 19, 5876.
15. Toffoli, G.; Viel, A.; Tuimoto, I.; Bisconti, G.; Rossi, G.; Baoiocchi, M. Br. J. Cancer
1991, 63, 51.
16. Dupuis, M.; Flego, M.; Molinari, A.; Cianfriglia, M. HIV Med. 2003, 4, 338.
17. Martello, L. A.; Verdier-Pinard, P.; Shen, H. J.; He, L.; Torres, K.; Orr, G. A.;
Horwitz, S. B. Cancer Res. 2003, 63, 448.
5.9.6. Western blot analysis
HeLa cells were incubated in the presence of test compounds
and, after different times, were collected, centrifuged and washed
two times with ice cold phosphate-buffered saline (PBS). The pellet
was resuspended in lysis buffer. After the cells were lysed on ice for
30 min, lysates were centrifuged at 15000ꢂg at 4 °C for 10 min. The
protein concentration in the supernatant was determined using
BCA protein assay reagents (Pierce, Italy). Equal amounts of protein
18. Hamel, E. Cell Biochem. Biophys. 2003, 38, 1.
19. Verdier-Pinard, P.; Lai, J.-Y.; Yoo, H.-D.; Yu, J.; Marquez, B.; Nagle, D. G.; Nambu,
M.; White, J. D.; Falck, J. R.; Gerwick, W. H.; Day, B. W.; Hamel, E. Mol.
Pharmacol. 1998, 53, 62.
(20 lg) were resolved using sodium dodecyl sulfate polyacrylamide
gel electrophoresis (SDS–PAGE) (7.5–15% acrylamide gels) and
transferred to a PVDF Hybond-p membrane (GE Healthcare).
Membranes were blocked with I-block (Tropix), the membrane
being gently rotated overnight at 4 °C. Membranes were incubated
with primary antibodies against, Bcl-2, Mcl-1, Xiap, cleaved cas-
pase-8, procaspase-2, PARP, cdc25C, Bax, survivin Thr34 and cdc2
(Tyr 15) (all rabbit, Cell Signalling, Milano, Italy), cyclin B1 (mouse,
BD, Milano, Italy) cleaved caspase-3 (mouse, Alexis) or b-actin
(mouse, Sigma–Aldrich, Milano, Italy) for 2 h at room temperature.
Membranes were next incubated with peroxidase-labeled goat
anti-rabbit IgG (Sigma–Aldrich, Milano, Italy) or peroxidase-
labeled goat anti-mouse IgG (Sigma–Aldrich) for 60 min. All mem-
branes were visualized using ECL Advance (GE Healthcare) and ex-
posed to Hyperfilm MP (GE Healthcare). To ensure equal protein
loading, each membrane was stripped and reprobed with anti-
b-actin antibody.
20. (a) Mollinedo, F.; Gajate, C. Apoptosis 2003, 8, 413; (b) Clarke, P. R.; Allan, L. A.
Trends Cell Biol. 2009, 19, 89.
21. Vakifahmetoglu-Norberg, H.; Zhivotovsky, B. Trends Cell Biol. 2010, 20, 150.
22. Mhaidat, N. M.; Wang, Y.; Kiejda, K. A.; Zang, X. D.; Hersey, P. Mol. Cancer Ther.
2007, 6, 752.
23. Ho, L. H.; Read, S. H.; Dorstyn, L.; Lambrusco, L.; Kumar, S. Oncogene 2008, 27,
3393.
24. Bhalla, K. N. Oncogene 2003, 22, 9075.
25. Wertz, I. E.; Kusam, S.; Lam, C.; Okamoto, T.; Sandoval, W.; Anderson, D. J., et al
Nature 2011, 471, 110.
26. Matson, D. R.; Stukenberg, P. T. Mol. Interv. 2011, 11, 141.
27. Altieri, D. C. Biochem. J. 2010, 430, 199.
28. Castedo, M.; Perfettini, J. L.; Roumier, T.; Andreau, K.; Medema, R.; Kroemer, G.
Oncogene 2004, 23, 2825.
29. O’Connor, D. S.; Grossman, D.; Plescia, J.; Li, F.; Zhang, H.; Villa, A.; Tognin, S.;
Marchisio, P. C.; Altieri, D. C. Proc. Natl. Acad. Sci. U.S.A. 2000, 9, 13103.
30. Viola, G.; Fortunato, E.; Cecconet, L.; Del Giudice, L.; Dall’Acqua, F.; Basso, G.
Toxicol. Appl. Pharm. 2008, 227, 84.
31. Ravelli, R. B. G.; Gigant, B.; Curmi, P. A.; Jourdain, I.; Lachkar, S.; Sobel, A.;
Knossow, M. Nature 2004, 428, 198.
32. Molecular Operating Environment (MOE 2010), Chemical Computing Group,
2012).
33. Korb, O.; Stützle, T.; Exner, T. E. LNCS 2006, 4150, 247.
34. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.;
Onufriev, A.; Simmerling, C.; Wang, C.; Woods, R. J. Comput. Chem. 2005, 26,
1668.
Acknowledgment
The authors would like to thank Dr. Alberto Casolari for excel-
lent technical assistance.
35. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14, 33.