Sustainability Challenges and Opportunities in Oligonucleotide Manufacturing

Abstract

With a renewed and growing interest in therapeutic oligonucleotides across the pharmaceutical industry, pressure is increasing on drug developers to take more seriously the sustainability ramifications of this modality. With 12 oligonucleotide drugs reaching the market to date and hundreds more in clinical trials and preclinical development, the current state of the art in oligonucleotide production poses a waste and cost burden to manufacturers. Legacy technologies make use of large volumes of hazardous reagents and solvents, as well as energy-intensive processes in synthesis, purification, and isolation. In 2016, the American Chemical Society (ACS) Green Chemistry Institute Pharmaceutical Roundtable (GCIPR) identified the development of greener processes for oligonucleotide Active Pharmaceutical Ingredients (APIs) as a critical unmet need. As a result, the Roundtable formed a focus team with the remit of identifying green chemistry and engineering improvements that would make oligonucleotide production more sustainable. In this Perspective, we summarize the present challenges in oligonucleotide synthesis, purification, and isolation; highlight potential solutions; and encourage synergies between academia; contract research, development and manufacturing organizations; and the pharmaceutical industry. A critical part of our assessment includes Process Mass Intensity (PMI) data from multiple companies to provide preliminary baseline metrics for current oligonucleotide manufacturing processes.

Green and sustainable chemistry – The case for a systems-based, interdisciplinary approach

“…As bioactive molecules common to the pharmaceutical industry, e.g., oligonucleotides, polypeptides, antibodies, drug-antibody conjugates, etc., become much larger and more prevalent, isolation and purification across compound synthesis and manufacture becomes an even bigger driver of process mass intensity ( Isidro-Llobet et al., 2019 ; Andrews et al., 2021 ). Solvent use is greater and the separation technology changes to solid phase linking and large-scale chromatographic processing in the place of distillation.…”

A P(V)-Platform for Oligonucleotide Synthesis

“…8 In the latter case, traditional methods make the key phosphate bonds unselectively, resulting in products being a mixture of diastereomers (up to 131,072 isomers for a standard 18-mer ASO), complicating product purification and the assessment of product quality. 9,10 In general, the P(III) method of synthesis also requires vast amounts of reagents and solvents, 11 both during oligo synthesis itself and during monomer formation, significantly impacting the sustainability for commercial manufacture -an aspect that is further complicated by the instability of the P(III) reagents themselves (which can be sensitive to both air and moisture). Methods for the asymmetric synthesis of ASOs suffer from even greater levels of environmental impact.…”

“…7% of the PS impurity resulting from desulfurization during the deprotection event. In contrast, utilizing y 2 , dimer (10) was cleanly accessed in two steps via P(V) adduct (11) in >99% purity. In order to field-test and contrast the synthesis of mixed PO/PS backbones by the two platforms, PS dimer (13) was subjected to a standard phosphoramidite coupling with (18) to yield protected trimer ( 14) which, upon oxidation of P(III) to the requisite P(V), resulted in rapid desulfurization [see ratio of (15)/(16) over time].…”

Avoiding High‐Pressure Problem for Modified RNA‐attached Polystyrene Support by Pre‐Swelling Using Toluene in the Oligonucleotide Synthesis

“…15 The overview of standard manufacturing process of ON has represented four key operations (Figure 1). 16 Synthesis operation is a solid-phase synthesis using solid support, phosphoramidite monomers, and process reagents for detritylation, coupling, oxidation, and capping steps. Once the synthesis is completed, Cleavage and Deprotection (C&D) process cleaves the full-length product from the solid support and removes the base-labile protecting groups by using a strong base solution, typically, aqueous ammonium hydroxide.…”