Y. Zhou et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2974–2978
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(A)
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15
16 17
(B)
1
2
3
4
5
6
7
8
9
10
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14
15
16
Figure 2. Topoisomerase I (A) and II (B) inhibitory activities of the tested compounds. All compounds were examined in a final concentration of 100
lM. (A) lane 1: relaxed
DNA only, lane 2: ScDNA + 1% DMSO, lane 3: ScDNA + Topo I, lane 4: ScDNA + Topo I + camptothecin, lane 5: ScDNA + Topo I + compound 5, lanes 6–17: ScDNA + Topo
I + compounds in order of 9d, 9k, 9e, 9g, 9i, 9f, 9l, 9a, 9b, 9c, 9h and 9j. (B) lane 1: relaxed DNA only, lane 2: ScDNA + Topo II, lane 3: ScDNA + Topo II + etoposide, lanes 4–7
and 9–16: ScDNA + Topo II + compounds as the same as the order of (A), lane 8: linear DNA only.
Figure 3. (A) Molecular docking between compound 9a and ATP-binding domain of human topo II
site of topo II are shown as sticks. The representation of the compound is colored by the atom type (carbon, orange; oxygen, red; nitrogen, blue; fluoro, cyan). (B) Molecular
docking between compound 9g and ATP-binding domain of human topo II
a. Compound 9a is depicted by stick. The key residues of the ATP-binding
a
a
. Compound 9g in stick representation is described as above.
3. Redinbo, M. R.; Stewart, L.; Kuhn, P.; Champoux, J. J.; Hol, W. G. Science 1998,
compound 9a occupies the ATP-binding site in an unreasonable
conformation, which would lead to increased internal energy. In
contrast, molecular docking study revealed compound 9g to have
a stable binding pattern to the ATP-binding domain, which was
matching with previously reported docking results of other topoi-
somerase II inhibitors.19 Compound 9g was found to has strong
intermolecular contacts with Arg 98, Gly164 and Ser149. The nitro
group attached to the benzene ring forms two hydrogen bonds
with Asn 150 and Arg 162. In addition, the fluoro atom substituent
forms a hydrogen bond with Thr 147 (Fig. 3B).
27, 504.
4. Chen, A. Y.; Liu, L. F. Annu. Rev. Pharmacol. Toxicol. 1994, 34, 191.
5. Kellner, U.; Rudolph, P.; Parwaresch, R. Onkologie 2000, 23, 424.
6. Singh, S. K.; Ruchebman, A. L.; Li, T. K.; Liu, A.; Liu, L. F.; Lavoie, E. J. J. Med. Chem.
2003, 46, 2254.
7. Fassberg, J.; Stella, V. J. J. Pharm. Sci. 1992, 81, 676.
8. Fox, B. M.; Xiao, X.; Antony, S.; Kohlhagen, G.; Pommier, Y.; Staker, B. L.;
Stewart, L.; Cushman, M. J. Med. Chem. 2003, 46, 3275.
9. Morrell, A.; Antony, S.; Kohlhagen, G.; Pommier, Y.; Cushman, M. J. Med. Chem.
2006, 49, 7740.
10. Pommier, Y. Nat. Rev. Cancer 2006, 6, 789.
11. Xiao, X.; Antony, S.; Pommier, Y.; Cushman, M. J. Med. Chem. 2006, 49, 1408.
12. You, Q. D.; Li, Z. Y.; Huang, C. H.; Yang, Q.; Wang, X. J.; Guo, Q. L.; Chen, X. G.;
He, X. G.; Li, T. K.; Chen, J. W. J. Med. Chem. 2009, 52, 5649.
The results of molecular docking indicated that the introduction
of electron withdrawing substituents into the benzene ring may
13. General procedure for the synthesis of intermediates 8a–8l: To a solution of the
Boc-protected Lomefloxacin (0.5 g, 1.1 mmol) in CH2Cl2 (20 mL) was added a
catalytic amount of DMAP (54 mg, 0.44 mmol) followed by TEA (0.5 mL,
3.3 mmol) and BOP (1 g, 2.2 mmol). The reaction mixture was allowed to stir
for 1 h at room temperature. After that a solution of amine (0.1 g, 1.1 mmol) in
CH2Cl2 (10 mL) was added dropwise and slowly to the mixture. The reaction
mixture was allowed to stir overnight at room temperature. Saturated
ammonium chloride aqueous solution (30 mL) was added and the reaction
was extracted with CH2Cl2 (3 ꢀ 20 mL). The organic layer was washed with
brine, dried over Na2SO4, filtered and concentrated. The product was then
purified over silica gel eluting with PET/EtOAc (1:1) to give pure 8a (0.29 g) in
50.1% yield. The compounds 8b–8l were similarly produced as 8a.
14. General procedure for the synthesis of the target compounds 9a–9l: A solution of
8a (0.2 g, 0.38 mmol) and CF3COOH (5 mL) in dry CH2Cl2 (20 mL) was stirred at
room temperature for 2 h. Saturated sodium bicarbonate solution (30 mL) was
added and the reaction was extracted with CH2Cl2 (3 ꢀ 10 mL). The organic
layer was washed with brine, dried over Na2SO4, filtered and concentrated. The
crude material was purified over silica gel eluting with CH2Cl2/MeOH (10:1) to
give the pure 9a (0.15 g) in 92.6% yield. The target compounds 9b–9l were
similarly produced as 9a.
anchor in the ATP-binding domain of human topoisomerase II
resulting in increased binding affinity, which lead to a higher topo-
isomerase II inhibitory activity.
In conclusion, we have designed and synthesized a series of
lomefloxacin derivatives and evaluated their pharmacological
activity. Of the compounds prepared compounds 9d, 9e, 9g, 9k,
9i and 9f could selectively impede topoisomerase II function with-
out affecting topoisomerase I catalytic activity. Molecular docking
study revealed compound 9g to have a stable binding pattern to
a
the ATP-binding domain of human topoisomerase IIa. This study
may provide valuable information to researchers working on the
development of novel antitumor agents targeting topoisomerase II.
References and notes
15. The data of selected compound 9d: yield 91.5%; mp 229–232 °C; IR (KBr): 3462,
1. (a) Wang, J. C. Annu. Rev. Biochem. 1996, 65, 635; (b) Berger, J. M. Biochim.
Biophys. Acta 1998, 1400, 3; (c) Kaufmann, S. H. Biochim. Biophys. Acta 1998,
1400, 195.
2969, 2845, 1680, 1605, 1563, 1471, 1376, 1318, 1296, 1022, 796, 649 cmꢁ1
;
EI-MS: 462 (M); 1H NMR (300 MHz, CDCl3): d 12.56 (s, 1H, –NH-CO), 8.59 (s,
1H, Ar-H), 8.24 (d, J = 1.9 Hz, 1H, Ar-H), 8.21 (s, 1H, Ar-H), 7.94 (d,
2. Pommier, Y. Biochimie 1998, 80, 255.