Quinoline-Based DNA Methyltransferase Inhibitors Featuring Basic Side Chains: Design, Synthesis, and Insight in Biochemical and Anticancer Cell Properties

The quinoline DNMT inhibitors 4–21, incorporating basic chains, were designed, synthesized, and evaluated for their ability to inhibit DNMT1 and DNMT3A/3L by directly measuring DNA methylation. Pharmacomodulation yielded nanomolar inhibitors with selectivity for either DNMT1 or DNMT3A/3L. The meta/meta analogs 7–14 exhibited the highest inhibition, with compounds 10 and 14 being the most potent and selective for DNMT3A/3L and DNMT1, respectively. DNA thermal denaturation experiments demonstrated for selected compounds strong DNA interaction. COBRA analysis in HCT-116 colon cancer cells revealed a selective reduction in P16INK4Amethylation, a tumor suppressor gene reactivated by DNMT inhibition. Among the tested cancer cell lines, HCT-116 was the most sensitive, and 14 showed the strongest antiproliferative effect. In isogenic HCT-116 P53–/–cells, 14 exhibited reduced antiproliferative activity, lower apoptosis, and decreased levels of cleaved Caspase 3, P53, and γH2AX, confirming its P53-dependent mechanism of action linked to DNA damage.