br Introduction DNA dependent protein kinase DNA PK
Introduction DNA-dependent protein kinase (DNA-PK) is a multicomponent serine/threonine protein kinase and considered a member of the phosphatidylinositol (PI) 3-kinase related kinase (PIKK family). This enzyme plays a critical role in the repair of mammalian DNA double strand breaks (DSBs) through the non-homologous end joining pathway of DNA repair , . It was proved that human cell lines defective in DNA-PK function are hypersensitive to agents that elicit DNA DSBs , . Selective DNA-PK inhibitors of DNA DSBs properties have potential application as radio and chemo potentiators in the treatment of cancer , , , , . Importantly, tumor cell lines defective in DSB repair as a consequence of compromised DNA-PK activity are highly sensitive to topoisomerase II inhibitors and ionizing radiation (IR) whereas over-expression of DNA-PKcs confers resistance to these agents by enhancing DSB repair . Taken together, these data provide compelling evidence that DNA-PK is an attractive therapeutic target for the modulation of DNA DSB repair in cancer therapy, and preliminary results with inhibitors have proved encouraging . In the drug discovery process, certain ligand-based approaches were introduced as advanced tools for design of new active hits , . Of these methods, 2D QSAR and pharmacophore modeling processes which in turn were able to predict the activity of proposed structures for saving the time and money . The validation procedures of the 2D and 3D models are essential for the whole protocol application and were indicated by different parameters like linearity of the correlation, root-mean-square error (RMSE), and the correlation factor, R2). Here, we report the design, synthesis, characterization, and modeling studies for novel small molecule DNA-PK inhibitors based upon structure-activity relationship analysis of different reference ligands , , , , . The protocol was designed through the insertion of different linker and terminal moieties to the reference L-27 structure that have potent DNA-PK inhibitory activity . The molecular docking of Vacuolin-1 receptor L-27 in the DNA-PK homology model revealed the importance of this side chain which was responsible for its activity. The interaction analysis showed stable bidirectional hydrophobic and hydrogen bonding interactions to Lysine, Arginine, and Serine residues. Different steps were followed subjecting the compound library resulted for pharmacophore analysis and activity prediction by 2D QSAR model, synthesized, and finally tested for both DNA-PK and cytotoxic screening, Fig. 1.
Methods and materials
Results and discussion
Molecular docking Based upon the previously homology model of the target DNA-PK ATP catalytic subunit, molecular docking experiments of the active compounds were done for investigation of their binding mode. The interaction analysis for our compounds with respect to the lead revealed an interesting pattern. Based on the docking results, our compounds could be clustered into two groups; the first group comprised the compound set 9a-f, and 11a-c appeared to share almost identical binding mode with that of the lead compound in which the benzoxazinone core being the main contributor for hydrogen bond networks. While the second group includes the compound derivatives possessing a terminal sulfonamide moiety 7b-f showed a similar binding mode to the lead, however, the sulfonamide terminal tail appeared to be extended and occupying an additional pocket not accommodated by the first group. The increased potency of compounds 7c and 9f from the activity table could be explained by the analysis of the docked poses, Fig. 6. The most potent compound from the first group 9f (2.5µM) showed a binding profile within the DNA-PK active site through three stable hydrogen bonds. The core benzoxazinone scaffolds share two bonds through nitrogen and carbonyl function moieties with the target residues Lys-3749 and Asp-3937 respectively. The third H-bond was established between carbonyl oxygen of linker and the residue Leu-3802. The extra binding mode of compound 9f than the lead one explained the importance of the acetamide linker which might be responsible for its activity and compound stability in the pocket. Compound 7c (most potent from the second group, 0.25µM) showed a binding mode similar to the lead compound with additional pocket furnishing interactions through sulphonamide tail. This compound exhibited specific binding mode by forming four set of hydrogen bonds. The benzoxazinone carbonyl oxygen and nitrogen atoms established dual hydrogen bonds with the critical catalytic residue Arg-3733. In addition, the two nitrogen atoms of the sulfonamide tail and the pyridine ring with the corresponding residue Tyr-3824 located within the additional pocket, Fig. 7. Fig. 8 summarized the pharmacophore points in the active compounds 7c and 9f compared to lead structure L-27.