Synthesis of a stable-isotope-labeled biotinylated pentasaccharide conjugate (EP217609), a dual-effect anticoagulant drug

EP217609 is a neutralizable dual‐effect anticoagulant under clinical investigation in cardiopulmonary bypass during cardiac surgery. Stable‐isotope‐labeled EP217609 was synthesized as an internal standard for mass spectrometry in support of bioassays. EP217609 was obtained in six steps starting from three building blocks in an overall yield of 42%, with a chemical purity of >99%. Thus, coupling between the N‐protected labeled biotin‐lysine 4, prepared in three steps from [13C,15N]‐l‐lysine 2, and the pentasaccharide‐spacer‐amine 6 was first performed. Removal of the Cbz protective group to 8 followed by coupling of the activated peptidomimetic building‐block 10 gave the immediate precursor of EP217609, which could be obtained after catalytic hydrogenolysis of 1,2,4‐oxadiazol‐5(2H)‐one into amidine. EP217609 is a neutralizable dual‐effect anticoagulant under clinical investigation in cardiopulmonary bypass during cardiac surgery. Stable‐isotope‐labeled EP217609 (SIL EP217609) was synthesized as an internal standard for mass spectrometry in support of bioassays. In this article, we report the synthesis and the characterization of SIL EP217609 which contains a pentasaccharide analog, fondaparinux, covalently bound to a peptidomimetic thrombin inhibitor and to a biotin entity.