A new highly efficient and eco-friendly protocol utilizing ultrasonic irradiation was established for the assembly of 2-amino-4H-pyran-3-carbonitriles series. Outstanding yields (97–99 %) and better reaction profiles were accessible utilizing the atom-economical approach. Further, three fused pyrimidines were accessible through cyclization reactions of 2-amino-5-oxo-4-(thiophen-2-yl)-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile (8 l) with various reagents under sustainable conditions. Moreover, the anti-proliferative activity of the assembled imidazopyrimidines was in vitro evaluated against three human cancer cell lines, MCF7 (breast cancer), HepG2 (liver cancer), and A549 (lung cancer), and one normal human cell line, MCF-10 A (human mammary cell line). In comparison to Doxorubicin, the criterion drug, all of the tested compounds exhibited potent cytotoxic effects. The relationship between activity and structure was also addressed. Noteworthy, the quantum chemical investigations of the assembled molecules using Density Functional Theory (DFT) have been studied and found to agree with the observed anti-proliferative activities. In addition, the docking studies demonstrated that the studied compounds possess low binding energies towards three selected proteins (6ENV-MCV-7, 4b3z-Lung, and HepG2-2JW2). Finally, the electron distribution on the surface of the assembled compounds has been evaluated by ESP.