Dual inhibitors of CDK2 and TRKA kinases: design, synthesis, antiproliferative activity and molecular modeling of novel pyrazolopyrimidine derivatives

Abstract

Simultaneous inhibition of CDK2 and TRKA presents a promising therapeutic avenue for cancer treatment, capitalizing on the critical roles of CDK2 in cell cycle regulation and TRKA in tumor cell survival and progression. In continuation of our previous work on dual CDK2/TRKA inhibitors, two series of pyrazolo[1,5-a]pyrimidines (6a–j, 9a–h) and pyrazolo[3,4-d]pyrimidines (11–13) comprising a total of 21 compounds were developed and assessed for their antiproliferative potential across 60 cancer cell lines of NCI. Among them, compound 9e exhibited broad-spectrum anticancer activity, inhibiting growth across all 60 cell lines with an overall mean %GI of 36.91%, showing maximal inhibition against SNB-75. The most active compounds were further evaluated for kinase inhibition. Compounds 6j and 6i displayed potent dual activity, with inhibitory potency (IC50) of 0.33 and 0.34 µM for CDK2, and 0.078 and 0.16 µM for TRKA, respectively. Both also showed strong antiproliferative effects against SNB-75, with IC50 values of 23.40 µM (6j) and 7.39 µM (6i) and against K562, with IC50 values of 42.28 µM (6j) and 14.08 µM (6i) and exhibiting a superior safety profile over Quercetin in normal fibroblasts. Cell cycle analysis of compounds 6i and 6j revealed significant arrest in the G2/M stage. Compound 6i induced the highest apoptosis (35.02%), dominated by late apoptosis (22.07%), and the highest necrosis level (7.10%), indicating more aggressive or less selective cytotoxicity. Overall, cell death was predominantly apoptotic, with limited necrotic contribution. Complementary docking studies confirmed that pyrazolopyrimidines adopted binding conformations similar to reference inhibitors within CDK2 and TRKA active sites. These findings highlight compounds 6i and 6j as promising dual CDK2/TRKA inhibitors for further development as anticancer therapeutics.