Development of a Kilogram-Scale Manufacturing Route for Bis-Tac-dG: Essential Building-Block for Guadecitabine

Abstract

Guadecitabine (SGI-110) is a dinucleotide that is a prodrug of decitabine. The dinucleotide contains decitabine (top fragment) and 2′-deoxyguanosine (9; dG; bottom fragment) connected via a 3′ → 5′ phosphodiester bond. The manufacturing process of guadecitabine requires a large quantity of N 2 , 3′-O-(4-tert-butylphenoxyacetyl)-protected dG (2; Bis-Tac-dG) to incorporate the bottom fragment. The protected 2 being a critical starting material of the dinucleotide imposes stringent quality requirements for its synthesis and isolation. Presented herein is the development work leading to a practical and scalable route for compound 2 starting from commercial dG. Salient features of the approach included one-pot protection of 5′-OH group of N 2 -Tac-dG (3) with 4,4′-dimethoxytrityl (DMT) group followed by 3′-O-Tac protection furnishing fully protected dG 8, thus reducing the cycle time with fewer isolation steps and lowering the solvent usage. Subsequently, cleavage of DMT group from 8 utilizing NaIO 4 enabled a mild, highly selective, and robust route to produce high purity (>99%) Bis-Tac-dG on kilogram-scale. The structure and origin of major impurities were determined by comparison with reference standards and carefully controlled to an acceptable level in compound 2. The improved synthesis was scaled to prepare multiple ∼60 kg batches of 2 to supply all clinical studies up to phase III.

Kilo-Scale Synthesis of the Dinucleotide DNA Methyltransferase Inhibitor Guadecitabine

“…The bis-Tac-dG ( 2 , 23.4 kg, 36.1 mol) is dissolved in DCM (approximately 129 kg) in an appropriate reactor at 5–25 °C. The solution is dried over a bed of 4 Å molecular sieves (3–12 kg) until the water content is ≤ 0.01% w/w as determined by Karl Fischer analysis.…”