New Quinoxaline-Based Derivatives as PARP-1 Inhibitors: Design, Synthesis, Antiproliferative, and Computational Studies

Abstract

Herein, 2,3-dioxo-1,2,3,4-tetrahydroquinoxaline was used as a bio-isosteric scaffold to the phthalazinone motif of the standard drug Olaparib to design and synthesize new derivatives of potential PARP-1 inhibitory activity using the 6-sulfonohydrazide analog 3 as the key intermediate. Although the new compounds represented the PARP-1 suppression impact of IC₅₀ values in the nanomolar range, compounds 8a, 5 were the most promising suppressors, producing IC₅₀ values of 2.31 and 3.05 nM compared to Olaparib with IC₅₀ of 4.40 nM. Compounds 4, 10b, and 11b showed a mild decrease in the potency of the IC₅₀ range of 6.35-8.73 nM. Furthermore, compounds 4, 5, 8a, 10b, and 11b were evaluated as in vitro antiproliferative agents against the mutant BRCA1 (MDA-MB-436, breast cancer) compared to Olaparib as a positive control. Compound 5 exhibited the most significant potency of IC₅₀; 2.57 µM, whereas the IC₅₀ value of Olaparib was 8.90 µM. In addition, the examined derivatives displayed a promising safety profile against the normal WI-38 cell line. Cell cycle, apoptosis, and autophagy analyses were carried out in the MDA-MB-436 cell line for compound 5, which exhibited cell growth arrest at the G2/M phase, in addition to induction of programmed apoptosis and an increase in the autophagic process. Molecular docking of the compounds 4, 5, 8a, 10b, and 11b into the active site of PARP-1 was carried out to determine their modes of interaction. In addition, an in silico ADMET study was performed. The results evidenced that compound 5 could serve as a new framework for discovering new potent anticancer agents targeting the PARP-1 enzyme.

Keywords: ADME parameters; MDA-MB-436; PARP-1 inhibitor; WI-38; antiproliferative; apoptosis; autophagy; cell cycle; molecular docking; quinoxaline.

Figure 1

Structures of PARP-1 inhibitors approved by FDA and others under clinical studies.

Figure 2

The three catalytic sub-pockets of PARP-1enzyme.

Figure 3

The design approach of the targeted quinoxaline-based derivatives 3–12 as PARP-1 inhibitors.

Scheme 1

Synthesis of different new quinoxaline-2,3-dione -based derivatives.

Scheme 2

Synthesis of different, new 2,3-dioxoquinoxaline-6-sulfonohydrazide-based derivatives.

Figure 4

Summary of SAR study for PARP-1 suppression effect of the most potent derivatives.

Figure 5

Cell cycle assessment of MDA-MB-436 before and after incubation with compound 5.

Figure 6

The percentage of cells in each phase was quantified using flow cytometry after PI staining of DNA. Data are presented as mean ± SD, n = 3.

Figure 7

(a) Control, (b) Apoptosis/necrosis assessment of MDA-MB-436 after incubation with compound 5. The four quadrants are identified as the necrosis quadrant (Q2-1), late apoptosis quadrant (Q2-2), normal intact cells (Q2-3), and early apoptosis quadrant (Q2-4). Different cell populations were plotted as a percentage of total events. Data are presented as mean ± SD; n = 3.

Figure 8

Apoptosis induction analysis caused by compound 5.

Figure 9

Autophagic cell death assessment in MDA-MB-436 cells after exposure to compound 5.

Figure 10

The 2D interaction diagrams of Olaparib and the five potent compounds 4, 5, 8a, 10b, and 11b.

Figure 11

The binding modes of Olaparib (I), 4 (II), 5 (III), 10b (IV), 8a (V), and 11b (VI). The compounds are shown as sticks, proteins as a cartoon, and the interacting amino acids as lines.

Figure 12

Left: Bioavailability radar from swissADME web tool for compounds 4, 5, 8a, 10b, and 11b. The pink area exhibits the range of the optimal property values for oral bioavailability and the red line is the predicted properties for each compound. Saturation (INSATU), size (SIZE), polarity (POLAR), solubility (INSOLU), lipophilicity (LIPO), and flexibility (FLEX) Right: Predicted Boiled-Egg plot for the compounds.