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Growing Oligonucleotide Chains More Sustainably

Honored Contributor
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By Isamir Martinez, Ph.D., PMP, Scientific Alliances & Business Engagement Manager, ACS Green Chemistry Institute; Stefan Koenig, Ph.D., Senior Scientist, Genentech; and, Ben I. Andrews, Investigator of Chemical Development, Product Development & Supply, GlaxoSmithKline

Aiming to employ oligonucleotides (ON), which are short deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules, as medical remedies has been a goal of scientists and physicians for some time.  As genetic information is carried forth from DNA through RNA, and eventually to the protein output via the central dogma of biology, there exist invaluable opportunities to address illness before it manifests itself.  During the COVID-19 pandemic, encouraging messenger RNA (mRNA) vaccines have come to the fore, with two distinct versions receiving emergency approval and currently leading the charge in vaccinating millions of people.  Beyond the sensational headlines, ONs have steadily been gaining ground as therapeutics since the approval of the first one in 1998.  Since then, more than 10 additional ON drugs have been delivered to patients and hundreds more are in clinical trials and preclinical development stages.

Therapeutic ON compounds take the form of single-stranded antagomirs, aptamers, gapmers, and splice-switching sequences, as well as double-stranded small interfering RNAs (siRNAs) and unconventional binding of ONs to Toll-like receptors (Hum. Gene Ther. 2015, 26, 475–485).  Constructing these ONs primarily relies on well-established solid-phase ON synthesis (SPOS) whereby the sequence of nucleotides is grown by iterative detritylation, coupling, oxidation, and capping (Figure 1), followed by cleavage, deprotection, purification, and isolation.  These tested manufacturing processes reliably deliver the ON products but they also consume extraordinary resources along the way.  The current state of the art in ON production utilizes large amounts of hazardous reagents and volumes of solvents via energy-intensive synthesis, purification, and isolation practices.  Since these manufacturing processes are costly and environmentally unsustainable, they limit the potential growth of ON therapeutics.

Figure 1: Oligonucleotide synthesis cycle. J. Org. Chem. 2021, 86, 49-61Figure 1: Oligonucleotide synthesis cycle. J. Org. Chem. 2021, 86, 49-61


The ACS Green Chemistry Institute Pharmaceutical Roundtable (GCIPR) has identified the development of greener processes for ON Active Pharmaceutical Ingredients (APIs) as a critical unmet need.  A focus team was created with the objective of identifying green chemistry and engineering improvements that would make ON production more sustainable. This group of scientists recently published a paper outlining the current approach and challenges in ON synthesis, purification, and isolation (J. Org. Chem. 2021, 86, 49-61).  They highlighted potential solutions to encourage synergies between the pharmaceutical industry, academia, and contract research, development and manufacturing organizations.  In addition to this perspective, the report also examined the quantitative waste impact of ON manufacturing via Process Mass Intensity (PMI) data from multiple roundtable members.  This investigative study provided a preliminary baseline expectation for current ON manufacturing and identified opportunities to reduce the waste impact.  In the process, it demonstrated that though they are synthetically produced, ONs have PMI values on the order of 4,300 kg of waste per kg of API produced.  This is in contrast to more traditional small molecules which often have PMIs an order of magnitude smaller.

With ON therapeutics filling industry pipelines to complement the traditional synthetic small molecule and biologic large molecules, the sustainability ramifications of these orthogonal modalities will grow in importance.  The waste burden inherent in current ON manufacturing processes will need to be addressed in order to improve the sustainability of ONs or growth of this promising class of therapeutic advances could be stunted.  This is true both as a cost of goods issue but also in terms of the impact on the environment.  We invite you to learn more about greening ON synthesis on our website: and join us to help accelerate the implementation of more sustainable ON processes.