Design and Synthesis of Ketenimine Sulfonamide Conjugates through Multicomponent Reactions; A Combined Cytotoxic Analysis and Computational Exploration

Abstract

Multicomponent reactions involving zwitterion generated from dimethyl acetylenedicarboxylate, aryl sulfonamide, and isocyanide to generate sulfonamide-conjugated ketenimines is reported. The synthetic strategy adopted is highly atom economical and stereoselective. Ketenimine sulfonamide analogues are key intermediates for further synthetic conversions to generate a combinatorial library of compounds. Furthermore, sulfonamide compounds are known to possess a broad spectrum of biological applications. All the novel molecules synthesized exhibit the potential to target the nonhomologous DNA end-joining (NHEJ) pathway with cytotoxic ability. Computational studies compliment the in vitro biological assays of the 8 small-molecule inhibitors. DNA double-strand breaks (DSBs) are considered as the most lethal among different DNA damages. NHEJ repairs about 70% of the DSBs generated in cells within mammals. The DNA-dependent protein kinase catalytic subunit is one of the PI3 kinases associated with NHEJ. Compounds DK01-DK08 were investigated for their ability to induce cancer cell death by treating with two leukemic cell lines where NHEJ is high. Results showed that bromoaryl (DK04)- and nitroaryl (DK05)-conjugated molecules showed excellent biological activity, having IC₅₀ values of ∼2 μM in Nalm6 cell lines.

Figure 1

(a) Optimized structure of DK01. (b) Structure (generated using Gauss view software) of the ketenimine sulfonamide derivatives synthesized by Shaabani et al. The structure is from ref (55) and is reproduced after copyright permission from the Royal Society of Chemistry [2011].

Figure 2

HPLC profile of DK03.

Figure 3

Bar diagram showing cytotoxicity of DK series in the Nalm6 cell line. Cells were treated with increasing concentrations of the compounds (1, 2, 5, 10, 50, and 100 μM) for 48 h. Control cells were treated with equivalent DMSO. Bar graphs for Nalm6 were plotted using % of viable cells and concentration of compounds.

Figure 4

Bar diagram showing cytotoxicity of DK series in CEM cell line. Cells were treated with increasing concentrations of the compounds (1, 2, 5, 10, 50, and 100 μM) for 48 h. Control cells were treated with equivalent DMSO. Bar graphs for CEM were plotted using % of viable cells and concentration of compounds.

Figure 5

Aligned docking poses of (a) DK01, DK02, DK03, and (b) DK04, DK05 compounds, respectively, in the active site of the protein kinase. Protein residues and DK ligands are shown by ribbon and ball/stick representations, respectively. The specific DK compound can be identified from its colored labels.

Figure 6

3D representation of the best docking pose highlighting the interactions between the DK01 compound (stick representation) and active site amino acid residues (ball and stick representation) of the protein kinase.

Figure 7

RMSD plots of (a) DK01–DK03 complex structures and (b) DK04–DK05 complex structures in the MD trajectory.

Figure 8

RMSF of protein residues in (a) DK01–DK03 complexes and (b) DK04–DK05 complexes in the MD trajectory.

Figure 9

(a) Significant hot spot and bad contact (residue id’s) with negative and positive energy contributions, respectively, to the total MM-PBSA binding energy of the DK01 complex. (b) Corresponding nonbonding interaction profile between the DK01 ligand residue and protein residues in its complex structure. Among these residues, the id of DK01–ligand residue is Lig4129 (b). Protein residues exhibiting hydrophobic and hydrogen bonded interactions with the ligand are labeled by red arcs and ball/stick representation with green dotted lines, respectively.

Figure 10

Significant hot spot and bad contact residue id’s with its energy value contributions, respectively, to the total MM-PBSA binding energy of (a) DK02 and (b) DK03 complexes.

Figure 11

Significant hot spot and bad contact residue id’s with their energy value contributions, respectively, to the total MM-PBSA binding energy of (a) DK04 and (b) DK05 complexes.

Figure 12

Nonbonding interaction between ligand residue and protein residues in (a) DK02 and (b) DK03 complexes. Protein residues exhibiting hydrophobic and hydrogen bonded interactions with the ligand are shown by red arcs and ball/stick representation with green dotted lines, respectively.

Figure 13

Nonbonding interaction between ligand residue and protein residues in (a) DK04 and (b) DK05 complexes. Protein residues exhibiting hydrophobic and hydrogen bonded interactions with the ligand are shown by red arcs and ball/stick representation with green dotted lines, respectively.