The comparative study of two synthetic pathways for nucleoside phosphoantigens is reported herein. The first using esterification of the γ-phosphate of ATP is leading to low yields whereas the coupling of ADP–imidazolate intermediate with a monophosphate counterpart is more efficient. Using this second approach various analogues of ApppI and ApppH were obtained. We have also investigated the synthesis of (E)-2-methyl-4-(hydroxyl)but-2-en-1-ol from mesaconic acid.