oligonucleotide synthesis

Bill Jarvis on oligonucleotide synthesis

Feb 17, 2020

Bill Jarvis is featured in Pharmaceutical Technology’s “Designing Commercial-Scale Oligonucleotide Synthesis.”

Along with Isaiah Cedillo with Ionis and Tony Pavone with Stanford University, the group writes an overview of how oligonucleotides (oligos) are currently being synthesized at a larger scale. As the industry trend moves towards commercial-scale manufacturing, the article provides insight on how to continue to develop and optimize this strategy. Throughout the article, recommendations are made that gear towards facilities producing multiple products with little compound-specific process research.

The manufacturing processes being used to produce several of these molecules are built on the solid-phase phosphoramidite approach developed by Beaucage and Caruthers more than 35 years ago. Since then, there has been significant improvement and optimization of the raw and starting materials, reaction parameters, purification, and isolation processes used for oligonucleotides and oligonucleotide mimics.

Process Overview

In its simplest description, oligonucleotide manufacturing consists of only a few, basic unit operations: solid-phase synthesis, purification, and isolation. The earliest syntheses of oligonucleotide drug substance were performed via solid-phase couplings on controlled pore glass (CPG) in sparged bed reactors.

Chemical and Analytical Considerations

Solid-phase oligonucleotide synthesis consists of four basic steps:

  1. Detritylation to remove the 4,4’-dimethoxytrityl (DMT) protecting group
  2. Coupling to attach the activated phosphoramidite
  3. Sulfurization or oxidation to convert the internucleotide linkage to either a phosphorothioate or phosphate diester
  4. Capping to prevent any unreacted sites from elongating further.

Large-scale Data

Quantity and quality of material are of paramount importance, but waste and solvent consumption are also worth considering as the demand of oligonucleotide increases.

Process Development

Most of the deviations and process failures to date have been associated with equipment failure as opposed to a failure of the chemistry or process parameters. Thus, in choosing a process, simplification by limiting the number of manufacturing steps would be a route to minimizing process failure by reducing the number of potential mechanical failures and equipment errors.

Read the full article in Pharmaceutical Technology.