In vitro antitumor activity, molecular dynamics simulation, DFT study, ADME prediction, and Eg5 binding of enastron analogues

Abstract

The objective of this study is to evaluate a series of molecules based on cyclosulfamide as potential anticancer agents. Additionally, the study aims to analyze the obtained results through in silico studies; by conducting experiments and utilizing theoretical methods. In this context, we investigated the cytotoxic activity of enastron analogues on three human cell lines PRI (lymphoblastic cell line) derived from B-cell lymphoma. JURKAT (ATCC TIB-152) acute T cell leukaemia and K562 (ATCC CLL-243) is a chronic myelogenous leukaemia. Most of the tested compounds showed good inhibitory activity compared with the reference ligand (chlorambucil). The 5a derivative demonstrated the strongest effect against all cancer cells used. Furthermore, molecular docking simulations of the Eg5-enastron analogue complex revealed that studied molecules have the ability to inhibit the Eg5 enzyme, as evidenced by their calculated docking score. Following the promising results from the molecular docking study, the complex Eg5-4a underwent a 100 ns molecular dynamics simulation using Desmond. During the simulation, the receptor-ligand pairing demonstrated substantial stability after the initial 70 ns. In addition, we used DFT calculations to analyze the electronic and geometric characteristics of the studied compounds. The HOMO and LUMO band gap energies, and the molecular electrostatic potential surface were also deducted for the stable structure of each compound. Also, we studied the prediction of absorption, distribution, metabolism and excretion (ADME) of the compounds.

Fig. 1. Chemical structure of some Eg5 inhibitors.

Scheme 1. Multicomponent reaction synthesis of benzothiadiazinone dioxides.

Scheme 2. Mechanistic proposal for the synthesis of benzothiadiazinone dioxide.

Fig. 2. Representation of IC₅₀ values.

Fig. 3. Docked and co-crystalized enastron in Eg5 enzyme after self-docking calculation.

Fig. 4. Superimposition of the docked enastron derivatives in the active site.

Fig. 5. 3D left and 2D right binding disposition of compounds 1a and 4a after docking calculations in the active site of Eg5 enzyme. The amino acid residues were shown as stick model and H-bonds were shown as black lines.

Fig. 6. 3D left and 2D right binding disposition of compound 5a after docking calculations in the active site of Eg5 enzyme. The amino acid residues were shown as stick model and H-bonds were shown as black lines.

Fig. 7. Schematic representation of SAR and substituents effect on the antitumor activity.

Fig. 8. Superimposition of the docked compound 4a before MD simulation (0 ns) and after 100 ns running dynamic simulation in the active site. Compound 4a at 0 ns (green sticks) and 100 ns (pink sticks). The amino acid residues were shown as wire models.

Fig. 9. Protein and ligand root mean square deviation (PL-RMSD) obtained from the MD simulation trajectories.

Fig. 10. RMSF diagram of the amino acids of the Eg5 protein in the system studied 4a–Eg5 (protein residues that interact with the ligand are marked with green-colored vertical bars alpha-helical and beta-strand regions are highlighted in red and blue background).

Fig. 11. Protein–ligand contacts obtained from the MD simulation trajectories.

Fig. 12. Timeline representation of the interactions and contacts (H-bonds, hydrophobic, ionic, and water bridges) obtained from the MD simulation trajectories.

Fig. 13. Protein secondary structure elements (SSE) monitored throughout MD simulation: alpha-helical 22.10%, beta-strand 20.85%, total SSE 42.95%. (Alpha-helical and beta-strand regions are highlighted in red and blue backgrounds, respectively, and the loop regions are highlighted in white backgrounds).

Fig. 14. (HOMO, LUMO) orbitals and optimized structures (1a–9a) at B3LYP/6-31G(d,p) level using a contour threshold of 0.02 a.u in gas phase.

Fig. 15. MEP formed by mapping of total density over electrostatic potential in gas phase for all compounds (1a–9a).

Fig. 16. Drug likeness score estimation curve using Molsoft server.

Fig. 17. Radar related to physicochemical properties of the synthesized molecules and CLB drug.