Development of a stepwise solvent-gradient SMB process for continuous-mode purification of methoxyethyl nucleoside phosphoramidites to be used as the key building blocks of oligonucleotide drugs

Abstract

One of the commercially proven oligonucleotide-based drugs that can treat a variety of life-threatening diseases through gene-expression control is 2′-O-methoxyethyl (MOE) oligonucleotide. To keep the economical production of the MOE-oligonucleotide stable, it is important to establish an efficient process for recovering its corresponding monomer (MOE nucleoside phosphoramidites) in a large quantity at high purity from the output of the phosphitylation reaction based on using MOE nucleoside as a starting component. To address this issue, we pursued the development of an efficient simulated-moving-bed (SMB) process for continuous-mode recovery of monomer from the considered reaction output. First, the intrinsic parameters of monomer and impurities present in the reaction output were obtained through an inverse method using silica gel as an adsorbent. The resulting intrinsic parameters were then applied to the optimal design of the SMB process for monomer recovery, which revealed that its optimal configuration was a four-zone open-loop SMB configuration based on the installation of regeneration and re-equilibration zones for implementing a stepwise solvent-gradient method. Under such configuration, the optimal SMB operation parameters to maximize throughput while keeping high purity stable were determined using the relevant optimization tool based on column model and genetic algorithm. It was confirmed through the experimental run that the optimized SMB process could enable the continuous recovery of monomer from the considered reaction output with 99.6% purity while keeping the monomer loss close to zero. Finally, the developed SMB process in this article was found to increase throughput by more than 33 times, and reduce solvent usage by more than 89%, compared to the plant-scale batch chromatographic process currently in operation in related industries.