Novel group of tyrosyl-DNA-phosphodiesterase 1 inhibitors based on disaccharide nucleosides as drug prototypes for anti-cancer therapy

Figures & data

Table 1. Structural formulas and inhibitory activities for the investigated disaccharide nucleosides.

*R_x: substituting group, in case of “-“ R = H; Ade^Bz: N⁶-Benzoyladenine-9-yl; Gua^i-But: N²-Isobutyrylguanine-9-yl; Cyt^Bz: N⁴-Benzoylcytosine-1-yl; 5-F-Ura: 5-Fluorouracil-1-yl; 5-I-Ura: 5-Iodouracil-1-yl.

Figure 1. The main structural blocks of the single-stranded (A) and the hairpin (B) oligonucleotides.

Table 2. Cytotoxicity of inhibitors, topotecan and their combination for A-549 and WI-38 cell lines.

I: inhibitor; tpc: topotecan; SC: synergistic coefficient. The inhibitor 6 was dissolved in water. Other inhibitors were dissolved in DMSO. Red colour indicates inhibitors that enhance cytotoxicity of topotecan for A-549 cell line; blue colour: for the WI-38 line.

Figure 2. Topotecan dose-dependent action of the disaccharide nucleosides on A-549 (A) and WI-38 (B) viability according to the MTT-assay. Average data with error bars from three independent experiments.

Figure 3. (A) TDP1 reaction scheme with single-stranded biosensor. (B) Gel pictures of the TDP1 reaction products. The arrows indicate the positions of the initial substrate and the reaction product. Concentration of TDP1 was 1.5 nM, concentration of single-stranded substrate was 50 nM, and reaction time was 20 min.

Figure 4. The dependence of fluorescence anisotropy on inhibitor concentration (A) for inhibitors 4, 7, 10, 11, 21; (B) for inhibitors 6, 41. Average data with error bars from two independent experiments.

Figure 5. TDP1 action and possible inhibition strategies. Yellow shape represents TDP1; pentagon represents Top1 residue in vivo or BHQ in this study.

Figure 6. (A) Dependence of V_max on the concentration of inhibitor 41. (B) Dependence of K_M on the concentration of inhibitor 41.

Table 3. IC₅₀ values for selected inhibitors obtained on single-stranded and hairpin substrates.

Table 4. Type of inhibition and values of inhibition constant (K_I) for selected inhibitors.

Compound number	Single-stranded substrate		Double-stranded substrate
	Inhibition constant, KI, µM	Type of inhibition	Inhibition constant, KI, µM	Type of inhibition
4	0.3 ± 0.1	Mixed	0.2 ± 0.1	Mixed
6	7.9 ± 0.8	Noncompetitive	8.8 ± 0.9	Noncompetitive
7	0.9 ± 0.3	Mixed	0.3 ± 0.1	Mixed
10	1.7 ± 0.4	Mixed	3.1 ± 0.3	Mixed
11	0.2 ± 0.1	Mixed	0.3 ± 0.2	Mixed
21	0.3 ± 0.2	Mixed	0.4 ± 0.3	Mixed
41	0.6 ± 0.3	Uncompetitive	2.1 ± 0.5	Uncompetitive