Scaling oligonucleotide manufacturing for the cardiometabolic era

Inclisiran, which targets proprotein convertase subtilisin/kexin type 9 (PCSK9) for low-density lipoprotein cholesterol reduction, was the first cardiometabolic siRNA therapeutic to gain approval. Several additional siRNA candidates are advancing towards high-prevalence indications, including zilebesiran (angiotensinogen, hypertension), plozasiran (apolipoprotein C3, hypertriglyceridaemia) and olpasiran (Lp(a), elevated lipoprotein(a)).1,2 That scale of demand is unlikely to be met through incremental expansion of existing infrastructure and requires a fundamental rethink of how oligonucleotide drugs are manufactured.3 The industry is approaching an inflection point and the decisions made over the next few years will determine how effectively the clinical promise of siRNA will translate into reliable patient access at scale.

Solid-phase oligonucleotide synthesis (SPOS) has been the industry standard for the last four decades. It is effective, well characterised, widely deployed and remains entirely adequate for programmes operating at a clinical scale or targeting small patient populations. However, SPOS was not originally developed for the manufacturing volumes anticipated for cardiometabolic indications. Current packed-bed flow synthesiser technology is generally limited to batch sizes of approximately 10kg per run. Scaling beyond this threshold becomes challenging due to physical constraints, including channelling, uneven residence time distribution and high pressure drop, all of which can compromise process control and batch-to-batch reproducibility.4 Producing one tonne of siRNA active pharmaceutical ingredient (API) using this technology today would therefore require running and pooling approximately 100 individual batches.

Environmental sustainability compounds the challenge. SPOS consumes large volumes of organic solvent and reagents, with process mass intensity (PMI) values routinely exceeding 3,000kg of raw material per kilogram of API produced.5 As production volumes increase, the environmental and regulatory burden associated with this level of waste becomes increasingly difficult to manage. Quality limitations are especially apparent for longer oligonucleotide sequences. Each successive coupling step introduces a small probability of incomplete reaction or side reactions, and these errors accumulate throughout the synthesis. For conventional 21 to 23mer siRNA strands, these limitations are generally manageable. However, longer constructs such as ~100-nucleotide single guide RNA or >150-nucleotide prime editing guide RNA used in clustered regularly interspaced short palindromic repeats-based gene editing applications present a substantially greater challenge, as accumulation of truncated sequences and related impurities can severely compromise yield and batch-to-batch consistency.

The result is a modular manufacturing strategy that improves scalability while leveraging existing SPOS infrastructure. Chemoenzymatic ligation has already been applied to manufacture GalNAc-conjugated PCSK9-targeting siRNA therapeutics relevant to cardiometabolic disease and at the end of last year, Alnylam Pharmaceuticals announced a $250 million investment in its Norton facility to support enzymatic assembly of siRNA therapeutics, including zilebesiran.7,8 Programmes at this scale require large-scale production of oligonucleotide fragments, which continue to depend on SPOS as the upstream synthesis step.

As the field enters this new paradigm, scientists and engineers are investigating improved fragment synthesis technologies, including solid-phase stirred reactors and liquid-phase oligonucleotide synthesis approaches, which may enable batch sizes to expand beyond the current ~10kg SPOS ceiling towards theoretical scales exceeding hundreds of kilograms per batch.9,10 Together with enzymatic ligation, improved fragment synthesis methods will likely form the foundation of manufacturing platforms capable of supporting multi-tonne commercial supply.

Enzymatic oligonucleotide synthesis represents a further potential evolution in the field. In these systems, engineered polymerases iteratively couple nucleoside triphosphates using mechanisms analogous to biological DNA and RNA synthesis.11,12 Recent studies have demonstrated the feasibility of biocatalytic synthesis of chemically modified RNA, and although the technology is not yet ready for industrial deployment, its long-term potential for scalable and sustainable manufacturing is substantial.13,14

Manufacturing technology advances are not the only area requiring innovation. Supply chain structure has a direct impact on quality, timelines and the practical ability to scale manufacturing operations. In conventional oligonucleotide manufacturing, production is typically distributed across multiple vendors. Separate organisations may supply phosphoramidites, solid supports, GalNAc and other raw materials, while others perform API synthesis and drug product formulation. The operational complexity associated with these distributed workflows becomes increasingly difficult to manage as programmes scale.

A vertically integrated supply model consolidates operations from raw material production to drug substance synthesis and drug product manufacturing within a coordinated manufacturing environment. Reduced organisational interfaces simplify project coordination, documentation management and operational oversight. Lot-level traceability can also be maintained continuously from raw materials through to the final released API or finished drug product, simplifying both investigations and regulatory submissions. Process changes, deviations and corrective actions can be managed within a unified quality system, reducing the delays often associated with distributed manufacturing networks. Vertical integration also supports more predictable cost management. Alignment between raw material production and downstream manufacturing reduces exposure to external pricing volatility and allocation constraints, minimising supply uncertainty. For programmes approaching commercial scale, this predictability becomes increasingly important.

Even with advances in synthesis technology and manufacturing integration, meeting future oligonucleotide demand will ultimately require substantial expansion of physical manufacturing capacity. Capacity investment must be planned years in advance because the timelines associated with facility construction, equipment procurement, process validation and regulatory approval are inherently long. Manufacturers that delay investment may struggle to support late-stage clinical programmes and commercial launches within the timelines developers require.

These risks became particularly visible during the pandemic and remain a major concern for drug developers. Manufacturers expanding across multiple regions, including facilities operating under US, European and Asian current good manufacturing practice standards, are better positioned to maintain supply continuity during regional disruptions. Regional manufacturing can also reduce the logistical complexity and lead times associated with international transport of temperature-sensitive materials.

Sustainability is increasingly integrated into capacity planning decisions. New facilities provide an opportunity to incorporate renewable energy systems, solvent recovery infrastructure and more resource-efficient manufacturing processes from the outset. In oligonucleotide manufacturing, technologies that reduce PMI, including liquid-phase synthesis and chemoenzymatic ligation, can be incorporated directly into facility design rather than retrofitted later. This improves environmental performance while reducing the long-term operating cost base of commercial supply.

The siRNA scaling challenge is not unique. Other oligonucleotide modalities, including multivalent siRNA, antibody oligonucleotide conjugates and guide RNAs for gene editing, will move through similar transitions as clinical validation expands and larger patient populations become addressable. Molecular architectures are becoming increasingly complex and manufacturing technologies need to evolve alongside them. Scalable approaches with greater reliance on biocatalysis and increasingly integrated manufacturing platforms are likely to become important components of future oligonucleotide production facilities.

Greater supply chain integration across raw material production, API and drug product manufacturing will become increasingly beneficial as developers seek to reduce operational complexity and reduce the cost of goods at a commercial scale. Regional manufacturing resilience, including the ability to maintain continuity of supply across changing regulatory, political and trade environments, is further factoring into this strategic planning. What is being built today defines not only the future of siRNA therapeutics, but also the broader foundation supporting the next generation of RNA medicines.

David Butler PhD, is chief technology officer at Hongene Biotech. David has previously led chemistry organisations at oligonucleotide companies, including Wave Life Sciences, Alltrna and Korro Bio. Earlier, he contributed to early lipid nanoparticle technologies at Alnylam Pharmaceuticals, helping advance platforms that laid the groundwork for today’s mRNA delivery systems. His current work focuses on manufacturing technology platforms and strategies to make RNA therapeutics globally accessible and affordable at commercial scale.

Scaling oligonucleotide manufacturing for the cardiometabolic era

David Butler at Hongene Biotech siRNA therapeutics are moving from niche to mainstream

Why solid-phase oligonucleotide synthesis will struggle to support cardiometabolic active pharmaceutical ingredient demand

Next-generation manufacturing technologies designed to scale

The case for vertically integrated supply chains

Manufacturing capacity expansion and regional resilience

Building the infrastructure to support the next generation of RNA medicines

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