(605c) Process Bottleneck of Packed Bed Oligonucleotide Reactors Arising from Critical Flux Due to Solid Phase Compressibility

Oligonucleotides have received growing attention as a new class of therapeutic. To date, over ten therapeutic oligonucleotides have hit the market and more than hundred are under clinical development. Some oligonucleotides under development have broad target patient population and are expected to have annual demand of over 1 metric ton. At present, solid phase oligonucleotide synthesis in packed bed reactors is the main manufacturing approach. The bed height is usually limited below 10 cm. Over-pressurization often occurs in the first 1 or 2 cycles when using polystyrene resin if running with a bed height that would eventually reach 10 cm by the end of the oligonucleotide build, which poses a major bottleneck for process throughput.

In this work, we have studied the pressure drop across a packed bed of polystyrene resin for oligonucleotide synthesis and quantified critical flux as a function of bed height, solvent, and length of oligo. We have found that the relationship between pressure drop and flux is nonlinear and the pressure drop increases exponentially as the flux reaches a certain critical value. We have also found that the packed bed is compressible under flow – bed height decreases as flux increases. Factors impacting the critical flux include the solvent, the bed height, the bed diameter and the length of oligonucleotide on resin. The more the solvent swells the resin, the lower the critical flux is in that solvent. The taller the bed, the lower the critical flux. The critical flux decreases as the bed diameter increases until it reaches around 2.5 cm. The longer the oligonucleotide on resin, the higher the critical flux (smaller specific cake resistance). We developed a mathematical model by considering bed compression under pressure drop and corresponding change in local porosity. This model can quantitatively describe our experimental data. We also developed a novel synthesis condition that allows detritylation reaction to be conducted in acetonitrile instead of toluene. There are already commercially available ACN-rich oxidation and sulfurization reagents. Performing detritylation in acetonitrile, together with those ACN-rich oxidation and sulfurization reagents, and with less concentrated capping reagents, over-pressurization problem can be made less severe, bed height can be higher, more solid phase can be packed in reactor, and therefore process throughput can be greatly increased.