Design, synthesis, and biological evaluation of Pyrido[1,2-a]pyrimidin-4-one derivatives as novel allosteric SHP2 inhibitors

SHP2 (Src homology-2-containing protein tyrosine Phosphatase 2) plays an important role in cell proliferation, survival, migration by affecting RAS-ERK, PI3K-AKT, JAK-STAT signaling pathways and so on. Overexpression or gene mutation of SHP2 is closely linked with a variety of cancers, making it a potential therapeutic target for Cancer disease. In this paper, 30 target compounds bearing pyrido[1,2-a]pyrimidin-4-one core were synthesized via two-round design strategy by means of scaffold hopping protocol. It was evaluated the in vitro enzymatic inhibition and cell antiproliferation assay of these targets. 13a, designed in the first round, presented relatively good inhibitory activity, but its molecular rigidity might limit further improvement by hindering the formation of the desired "bidentate ligand", as revealed by molecular docking studies. In our second-round design, S atom as a linker was inserted into the core and the 7-aryl group to enhance the flexibility of the structure. The screening result revealed that 14i could exhibit high enzymatic activity against full-length SHP2 (IC₅₀ = 0.104 μM), while showing low inhibitory effect on SHP2-PTP (IC₅₀ > 50 μM). 14i also demonstrated high antiproliferative activity against the Kyse-520 cells (IC₅₀ = 1.06 μM) with low toxicity against the human brain microvascular endothelial cells HBMEC (IC₅₀ = 30.75 μM). 14i also displayed stronger inhibitory activities on NCI-H358 and MIA-PaCa2 cells compared to that of SHP099. Mechanistic studies revealed that 14i could induce cell Apoptosis, arrest the cell cycle at the G0/G1 phase and downregulate the phosphorylation levels of Akt and ERK1/2 in Kyse-520 cells. Molecular docking and molecular dynamics studies displayed more detailed information on the binding mode and binding mechanism of 14i and SHP2. These data suggest that 14i has the potential to be a promising lead compound for our further investigation of SHP2 inhibitors.

Anti-proliferation; Inhibitors; Pyrido[1,2-a]pyrimidin-4-one; SHP2.