Synthesis, anticancer evaluation and molecular docking studies of new benzimidazole- 1,3,4-oxadiazole derivatives as human topoisomerase types I poison

Figures & data

Figure 1. Hoechst 33258 and Hoechst 33342 compounds.

Table 1. Hydrogen and carbon values of compound 5e detected by 2 D NMR.

Position	^1H	^13C
1	6.68	111.0
2	8.39	158.5
3	–	161.4
4	3.60–3.86	42.0–45.5
5	3.65–3.77	43.4–43.7
6	–	165.4
7	4.62	37.3
8	–	152.3
9	–	165.3
10	–	136.0
11	7.98	123.6
12	7.86	115.4
13	8.15	112.3
14	–	119.7
15	–	134.0
16	–	164.2
17	–	114.8
18	8.22	130.7
19	7.06	116.9
20	–	162.8
21	10.88	–
22	12.69	–

Table 2. IC₅₀ values (µM) of the compounds 5a-5o, doxorubicin and Hoechst 33342 against A549, MCF-7, C6, HepG2, HeLa and NIH3T3.

Bileşik	A549	MCF-7	C6	HepG2	HeLa	NIH3T3
5a	43.256 ± 1.785	5.704 ± 0.254	15.614 ± 0.615	5.695 ± 0.283	13.960 ± 0.65	39.105 ± 1.940
5b	≥100	≥100	≥100	≥100	0.698 ± 0.032	944.360±7.625
5c	≥100	≥100	≥100	21.860±0.991	20.285±1.101	44.556±0.221
5d	≥100	9.148 ± 0.391	38.93±1.921	≥100	≥100	720.645±5.032
5e	≥100	7.318 ± 0.352	≥100	≥100	≥100	54.026±2.682
5f	≥100	≥100	≥100	≥100	≥100	–
5g	≥100	≥100	≥100	≥100	≥100	–
5h	≥100	≥100	≥100	≥100	≥100	–
5ı	≥100	≥100	≥100	≥100	≥100	–
5j	≥100	≥100	≥100	≥100	≥100	–
5k	22.254 ± 1.054	38.705±1.875	3.204 ± 0.152	≥100	11.167±0.467	74.630±3.631
5l	31.017 ± 1.530	≥100	≥100	≥100	0.224 ± 0.011	113.451±5.472
5m	≥100	≥100	32.167±1.552	≥100	≥100	52.264±2.512
5n	7.388 ± 0.325	≥100	≥100	≥100	0.205 ± 0.010	188.570±8.728
5o	≥100	6.442 ± 0.287	24.951±1.237	59.369±2.589	≥100	44.072±2.104
Dox.	12.420±0.521	10.525±0.472	28.690±1.228	16.482±0.804	14.280±0.704	1110.80±8.254
Hoechst 33342	0.422±0.020	2.404±0.118	1.051±0.307	27.815±1.190	0.306±0.015	7.388±0.269

Figure 2. % DNA synthesis inhibition activities of compound 5n and doxorubicin against A549 cell line.

Figure 3. % DNA synthesis inhibition activities of compounds 5a, 5d, 5e, 5o and doxorubicin against MCF-7 cell line.

Figure 4. % DNA synthesis inhibition activities of compound 5a and doxorubicin against HepG2 cell line.

Figure 5. % DNA synthesis inhibition activities of compound 5k and doxorubicin against C6 cell line.

Figure 6. % DNA synthesis inhibition activities of compounds 5 b, 5 l, 5n and doxorubicin against HeLa cell line.

Figure 7. The flow cytometric analysis diagram of compound 5n and doxorubicin for A549 cell line.

Figure 8. The flow cytometric analysis diagram of compounds 5d, 5e, 5o and doxorubicin for MCF-7 cell line.

Figure 9. The flow cytometric analysis diagram of compound 5k and doxorubicin for C6 cell line.

Figure 10. The flow cytometric analysis diagram of compound 5a and doxorubicin for HepG2 cell line.

Figure 11. The flow cytometric analysis diagram of compounds 5 b, 5 l, 5n and doxorubicin for HeLa cell line.

Figure 12. Topo I activity of compounds 5a, 5 b, 5d, 5e, 5k, 5 l, 5n, 5o, Hoechst 33342 and camptothecin.

Figure 13. Three-dimensional interaction of Hoechst 33342 with the DNA-Topoisomerase I enzyme complex active site.

Figure 14. Docking poses of compound 5n. (A) Placement of the compound 5n on the DNA-Topoisomerase I enzyme complex active site. (B) The interacting mode of compound 5n in the active region of DNA-Topoisomerase I enzyme. (C) Van der Waals interaction of DNA-Topoisomerase I enzyme complex active site of compound 5n. (D) Electrostatic interaction of DNA-Topoisomerase I enzyme complex active site of compound 5n.

Scheme 1. Continued.

Table 3. Binding affinity and interacting residues of compound 5n and Hoechst.

Compounds	Binding affinity (Kcal/mol)			Interacting residues (According to Van der Waals, coulomb, hydrogen-bonding energies)
	Docking score	Glide gscore	Glide emodel
5n	−7.409	−7.889	−100.082	Asn352, Glu356, Arg364, Lys374, Lys425, Arg488, Lys493, Gly531, Lys532, Asp533, Ile535, Lys587, Arg590, Hid632, Gly717, Thr718, Asn722, DA7, DC8, DT9, DT10, DC111, DC112, DA113, DA114, DG115, DT116
Hoechst	−4.373	−5.989	−66.563	Asn352, Glu356, Phe361, Arg364, Lys374, Gln421, Ser423, Lys425, Arg488, Lys493, Lys532, Asp533, Lys587, Arg590, Hid632, Gly717, Thr718, Leu721, Asn722, DA7, DC8, DT9, DT10, DC111, DC112, DA113, DA114, DG115, DT116