Development of a Scalable, Racemic First-Generation Route for CXCR7 Antagonist ACT-1004-1239 via cis-to-trans Epimerization and Subsequent Separation of Enantiomers

The high structural complexity of CXCR7 antagonist ACT-1004-1239 turned the development of a scalable route into a formidable challenge. The presence of two stereocenters, the intermediacy of highly polar or fluorinated heterocyclic building blocks, and the extremely low solubility of the API were just three of the factors that contributed to this challenge. Given the high time pressure on the project, a racemic route was developed with priority in less than 12 months. The key to success was the synthesis of racemic N-Boc-3-methyl 4-aminopiperidine-3-carboxylate (cis:trans 2:1) and its isolation in high chemical purity as the crystalline TFA salt. After amide coupling with 5-(2,4-difluorophenyl)­isoxazole-3-carboxylic acid, the 3-position of the piperidine ring was fully epimerized to the more stable trans-isomer by using NaOMe. At this stage, the trans enantiomers were separated by liquid chromatography on a chiral stationary phase. The desired 3S,4S-enantiomer was recovered in excellent yield (48%, compared with theoretical 50%) and purity (e.r. 99.8:0.2). After a final sequence of saponification, amide coupling, Boc deprotection and reductive amination with cyclopropanecarboxaldehyde, the API was isolated as a white solid with high purity. Over 500 g of API was produced in-house for preclinical activities with this racemic route, which was also used to produce 5.5 kg of GMP material at an external manufacturing partner for Phase 1 clinical studies.