Large-scale supercritical fluid chromatography purification of unstable STING agonist intermediates

•Intermediate 1 and Intermediate 2 are two nucleoside derivatives, and required resolution by preparative supercritical fluid chromatography (SFC) to obtain the desired regioisomer as a key intermediate in a STING agonist program.•A key issue associated with interconversion between the regioisomers via silyl migration during purification was investigated in methanol, acetonitrile, and the mixture of acetonitrile and isopropanol, and the optimal organic modifier in CO2 was established to mitigate the interconversion to an acceptable level (