Green synthesis of novel Isatin derivatives, characterization, DFT and molecular dynamics studies, and anticancer detection as promising CDK2 inhibitors

A series of novel isatin derivatives ( BRI-1-BRI-4 ) was synthesized via a green and efficient synthetic approach and structurally characterized using standard spectroscopic techniques. The synthesized compounds were evaluated for their in vitro anticancer activity against the Michigan Cancer Foundation-7 (MCF-7) breast cancer cell line using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Among the tested compounds, BRI-4 exhibited the highest cytotoxic activity (IC₅₀ = 13.62 ± 0.52 µM), although it was less potent than the reference drug doxorubicin (IC₅₀ = 8.20 ± 0.76 µM). A preliminary structure–activity relationship (SAR) analysis of this limited series indicated that substituent-dependent electronic/halogen-related effects influenced the observed cytotoxic response, with BRI-4 showing the most favorable activity profile among the synthesized analogs. To gain molecular-level insight, density functional theory (DFT) calculations were performed to investigate optimized geometries and relevant electronic descriptors (including frontier molecular orbitals and related reactivity parameters), supporting the effect of structural variation on molecular behavior. In addition, molecular docking and molecular dynamics (MD) simulations were conducted using Cyclin-dependent kinase 2 (CDK2) as a biologically relevant target to explore possible binding interactions and complex stability. The in silico results suggested favorable binding of the synthesized compounds within the CDK2 active site, particularly for BRI-4 , and were consistent with the experimental activity trend. Overall, the combined synthetic, biological, and computational findings identify BRI-4 as the most active compound in this small series and a promising lead candidate for further optimization; however, direct CDK2 enzymatic inhibition and mechanistic cellular studies are required to validate the proposed mode of action.