Design, Synthesis, Computational Modeling and Biological Evaluation of Novel N‐( <scp>7</scp> <i>H</i> ‐Pyrrolo[2,3‐ <i>d</i> ]pyrimidin‐4‐yl)cinnamamides as Potential Covalent Inhibitors for Oncology

A novel series of covalent pyrrolo[2,3-d]pyrimidine cinnamamides was synthesized and evaluated for anticancer activity. The compounds were tested against three cancer cell lines-MDA-MB-231 (triple-negative breast cancer), A549 (non-small cell lung cancer), and U-87 MG (glioblastoma), alongside a cytotoxicity assessment on non-tumor NIH/3 T3 mouse embryonic fibroblast cell line. Compound 5k (IC₅₀ = 0.99 ± 0.45 μM) and 5i (IC₅₀ = 1.15 ± 0.14 μM) demonstrated markedly higher potency against MDA-MB-231 cells compared to cisplatin (IC₅₀ = 34.36 ± 0.16 μM), whereas 5e was found active against A549 cells (IC₅₀ = 1.41 ± 1.13 μM). None of the active compounds exhibited significant toxicity against normal NIH/3 T3 cells. Molecular docking studies involving covalent modification at the ATP-binding sites of EGFR (L858R/T790M), HER2, and JAK3 via key interactions with Cys797 (EGFR/HER2) and Cys909 (JAK3) supported their irreversible mechanism of action. Glutathione-binding assay confirmed the covalent adduct formation with a prominent molecular ion peak corresponding to the adduct. Density Functional Theory analyses of the leading compounds revealed low HOMO-LUMO energy gaps, which correlated with elevated electronic reactivity and biological capability. Electrostatic surface potential maps further highlighted distinct electrophilic character around the acrylamide warhead, facilitating potential covalent bond formation with nucleophilic Cys residues in the target proteins. In silico ADMET profiling confirmed favorable drug-likeness and safety attributes. Together, these findings support the discovery of this novel class of covalent pyrrolo[2,3-d] pyrimidine cinnamamides as promising and safer lead candidates for anticancer therapy, particularly against triple-negative breast cancer.