In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of Oncogene.

Overexpression of oncogene is associated with cancer pathology. Expression of is regulated by the G-quadruplex structure formed in the G-rich segment of nuclease hypersensitive element (NHE III), that is, "", which is localized in the promoter region. Ligand-induced stabilization of the structure has been identified as a novel target for cancer therapeutics. Here, we have explored the library of synthetic compounds against the predefined binding site of . Three compounds were selected based on the docking analyses; they were further scrutinized using all atom molecular dynamics simulations in an explicit water model. Simulated trajectories were scrutinized for conformational stability and ligand binding free energy estimation; essential dynamic behavior was determined using principal component analysis. One of the molecules, "TPP (1-(3-(4-(1,2,3-hiadiazol-4-yl)henoxy)-2-hydroxypropyl)-4-carbamoyliperidinium)", with the best results was considered for further evaluation. The theoretical observations are supported well by biophysical analysis using circular dichroism, isothermal titration calorimetry, and high-resolution NMR spectroscopy indicating association of TPP with . The in vitro studies were then translated into overexpression in the T47D breast cancer cell line. Biological evaluation through the MTT assay, flow cytometric assay, RT-PCR, and reporter luciferase assay suggests that TPP downregulates the expression of oncogene by arresting its promoter region. In silico and in vitro observations cumulatively suggest that the novel skeleton of TPP could be a potential anticancer agent by stabilizing the G-quadruplex formed in the and consequently downregulating the expression of oncogene. Derivation of new molecules on its skeleton may confer anticancer therapeutics for the next generation.