Identification of novel dual-specificity phosphatase 26 inhibitors by a hybrid virtual screening approach based on pharmacophore and molecular docking

Dual-specificity Phosphatase 26 (DUSP26) has recently emerged as a target for treatment of human cancers. However, only two small-molecule inhibitors of DUSP26 are known so far, namely NSC-87877 and ethyl-3, 4-dephostatin. DUSP26 contains an N-terminal region (residues 1-60) and a conserved C-terminal catalytic domain (residues 61-211, DUSP26-C). The crystal structure of DUSP26-C, showing a catalytically inactive conformation of the active site, was reported in a previous study. However, the detailed catalytic mechanism of DUSP26 cannot be described based on that structure. In this study, the 3D structure of DUSP26 (residues 42-211) adopting catalytically active conformation, was built by homology modeling, and the established 3D structure was validated using Enzyme kinetic assays. Pharmacophore modeling based on the validated 3D structure of human DUSP26 was carried out. The established pharmacophore model was considered as a 3D query for retrieving novel DUSP26 inhibitors from the chemical databases "Diversity Libraries" (129,087 compounds). Next, a docking study was performed to refine the obtained hit compounds. Then a total of 100 compounds were selected based on the ranking order and visual examination, which were then evaluated by an enzyme-based assay. Eight compounds were found to have inhibitory activities against DUSP26, and the most potent compound was assigned No. F1063-0967 with an IC₅₀ value of 11.62μM. The inhibitory activity of F1063-0967 against DUSP26 is higher than that of NCS87877 (IC₅₀ value: 16.67±2.89μM), but lower than that of ethyl-3, 4-dephostatin (IC₅₀ value: 6.8±0.41μM). MTT assay results revealed that F1063-0967 can induce Apoptosis in IMR-32 cell line with an IC₅₀ value of 4.13μM. These results suggest that F1063-0967 should be investigated further for other pharmacological properties.