Moderator: Sarah Richards, Publication Strategist at PFAm
Q. Oligonucleotide CMC has evolved beyond platform-driven development toward molecule-specific strategies. From your perspectives in technology leadership and CDMO science, how has the definition of “CMC readiness” changed, and where do you see sponsors still relying too heavily on legacy platform assumptions?
David: With the rapid expansion of oligonucleotide therapeutics into formats such as AOCs, novel conjugates, pegRNAs and multivalent constructs, CMC readiness is best de-risked by looking beyond SPOS and phosphoramidite-based platforms. Sponsors sometimes assume these processes will scale unchanged for these novel formats, but transitioning to next-generation technologies like chemoenzymatic ligation can offer significant quality and cost advantages. Early collaboration with experienced, technology-ready CDMOs helps challenge assumptions and mitigate operational and chemistry risks.
Q. Analytical characterisation requirements for oligonucleotides continue to expand.
Which analytical capabilities do you believe should be established earlier than sponsors typically plan, and where can a fit-for-purpose approach safely replace overengineering?
Lucia: From our experience working with early oligonucleotide programs, sponsors often introduce detailed impurity analysis and high-resolution LC–MS too late. These tools should be used earlier, even with fit-for-purpose methods, because they help guide chemistry and purification decisions. At the same time, sponsors can postpone full method validation and extensive stability testing, allowing early development to remain efficient while establishing methods that support later clinical and regulatory needs.
Q. Tech transfer from early-stage to larger-scale manufacturing is often a critical inflection point. What key data or process understanding is most frequently missing at this stage, and how can sponsors address these gaps earlier without slowing development?
David: A risk often encountered during tech transfer is that downscale models used in process development don’t accurately predict behavior at manufacturing scale. This is especially true for novel oligonucleotide formats, where process dynamics may shift significantly between scales and equipment. In addition, limited batch experience in early development can result in incomplete process understanding, leading to variability and out-of-specification (OOS) results at scale. Sponsors can mitigate these and other risks through close collaboration with experienced CDMO partners.
Lucia: At tech transfer, the main challenge is usually not a lack of data, but a limited understanding of how the process really behaves, and which parameters drive impurities and variability. Early processes are often designed with limited resources and are rather for speed than scale. Sponsors can reduce risk by capturing basic information on critical steps, impurity profile, and process limits early on, using simple, focused experiments and consistent documentation, without slowing development timelines. Thus, sponsors allow early development to remain efficient while building methods that support later clinical and regulatory needs.
Q. Early chemistry and sequence design decisions often determine long-term manufacturability and regulatory risk. Which chemistry or design choices during lead optimisation deserve greater scrutiny today to avoid downstream CMC bottlenecks and IND delays?
David: Chemistry and sequence design decisions during lead optimisation should ideally emphasise simplicity and manufacturability. Sequence-related risks can largely be avoided early through appropriate in silico screening at the target identification stage. Raw materials should be selected not only for functionality but also for their stability and cost-effective scalability. Similarly, modifications that compromise oligonucleotide stability or complicate purification should be avoided wherever possible. Chemically conservative, stable designs help de-risk development and support more efficient IND submissions.
Q. Sponsors increasingly push for speed in early oligonucleotide programs, sometimes at the expense of depth. Where do you most often see disconnects between discovery, developability, and early CMC, and what are the consequences later in development?
Lucia: One of the common disconnects we observe occurs when optimising sequences for biological performance with limited input from CMC or manufacturing. This can lead to difficulties in purification, low purity or unstable impurity profiles later. The consequence can be rework during scale-up or delayed timelines. Early collaboration between discovery, development, and CMC teams helps maintain speed while avoiding costly downstream problems.
Q. As oligonucleotide length, conjugation, and delivery complexity increase, sequence-related impurities remain a major challenge. From both a technology development and early manufacturing perspective, what chemistry or process innovations hold the most promise for impurity control at scale?
David: Chemoenzymatic ligation is a next-generation synthesis platform with demonstrated potential to reduce oligonucleotide impurities at scale. For example, Hongene’s ‘sticky-end’ and ‘splinted’ ligation workflows are well-suited to chemically modified siRNAs and single-stranded oligonucleotides, including pegRNAs, and consistently deliver cleaner products than traditional SPOS. Leveraging this technology, we routinely achieve >95% HPLC purity with no detectable ligation-related impurities for GalNAc-conjugated siRNAs and >90% purity for 100mer sgRNAs.
Q. Regulatory expectations for oligonucleotide CMC are rising, even in early clinical phases. Which CMC elements do sponsors most commonly underestimate when preparing IND submissions, and how should early development strategies adapt?
David: One of the most commonly underestimated areas in IND preparation is the level of molecular characterisation now expected by regulators, even during Phase 1. Sponsors may overlook the need to demonstrate robust control of critical impurities and, increasingly, stereochemical distribution for oligonucleotides containing chiral backbone linkages. Early integration of appropriately specific and sensitive analytical methods, with orthogonality where warranted, can help reduce regulatory surprises and support a smoother path to the clinic.
Lucia: Sponsors often underestimate how much detail regulators expect around impurity understanding and control, even in early INDs. Regulators want to see that impurities are not only determined but also explained. Early strategies should focus on clear links between process steps and impurity outcomes, using suitable analytical methods without full validation at this stage.
Xufeng: Sponsors often underestimate the analytical requirements of product characterisation and control strategy. A critical early development strategy is to develop analytical methods capable of providing comprehensive impurity profiling, identification and potency measurement. These methods should be orthogonal and applicable to both API and drug product manufacturing process control. For instance, developing a stability-indicating method early in the process is recommended, as it can support stability study, terminal sterilisation feasibility study and product hold time evaluation.
Q. As oligonucleotide therapeutics move toward greater molecular complexity and faster clinical timelines, what is the single early-stage CMC or manufacturing decision that most strongly determines long-term program success - and why?
David: Long-term program success depends on high-quality, risk-mitigated and scalable manufacturing. Arguably, the most critical early decision is selecting a vertically integrated CDMO to eliminate the vulnerabilities of a fragmented supply chain. Engaging early with a partner offering end-to-end control enables better assessment of manufacturability and quality risks, setting the foundations for a smoother clinical life cycle and stronger commercial viability.
Lucia: One of the most important early decisions is choosing a scalable manufacturing and purification approach that can control impurities, along with choosing an experienced manufacturer or CDMO. Early choices around chemistry, purification, and analytical control shape cost, quality, and regulatory risk throughout development. An experienced CDMO helps anticipate scale-up challenges and regulatory expectations early, reducing rework and delays in timelines.
Xufeng: Defining the API starting material and synthetic process early in the program has the most impact on long-term success. The definition of starting materials for oligonucleotide is more complex than for small molecules. This decision directly impacts the development of analytical methods and process validation. Changes to the starting material definition and API synthetic process in later development phases can necessitate repeating analytical work and conducting comparative bridging studies, which can affect regulatory filings, program timeline, and overall cost.
Q. Oligonucleotide development is increasingly shaped by external pressures - compressed timelines, capital efficiency, supply-chain constraints, and evolving regulatory scrutiny. How should sponsors prioritise which CMC risks to solve early versus which can be deferred without jeopardising program viability, and where do you most often see teams getting this prioritisation wrong?
David: Sponsors should prioritise CMC activities through robust risk assessments to align with phase-appropriate manufacturing strategies and safety. Common pitfalls include underestimating raw material supply chain risks for novel linkers or conjugates, overcommitting to analytical method validation too early and inadequate characterisation of critical impurities. Teams might also misjudge manufacturing volumes or delay booking slots at CDMOs, leading to avoidable setbacks. A risk-based approach that is tightly aligned with clinical and non-clinical safety requirements helps avoid unnecessary delays and control costs.
Lucia: Sponsors should focus early on risks that are difficult to change later, such as sequence design, chemistry platform, and manufacturing approach, supported by robust, fit-for-purpose analytical methods, even if they are not yet fully validated. Activities like formal validation and late-stage optimisation can be handled later. Teams often misprioritize by emphasising early compliance or speed while underinvesting in analytical and process understanding, which can lead to struggles during scale-up and later regulatory overview.
Xufeng: Early priority should be given to establishing a scalable API synthesis process, developing appropriate analytical methods, defining CQA for API and drug product, and securing the supply chain for key materials. Certain activities can be deferred without jeopardising the program, including detailed optimisation of yield and process efficiency, and full method validation. Common pitfalls observed include challenges in qualifying raw material vendors, resulting in the program delay, and inconsistencies in drug product concentration control due to an inadequate analytical method for potency measurement.
Thank you, David, Lucia, and Xufeng, for sharing your expert insights on the evolving landscape of oligonucleotide CMC and manufacturing. Your perspectives on process development, scale-up strategies, regulatory expectations, and operational excellence have provided valuable clarity on both the current challenges and the future direction of this rapidly advancing field.
We truly appreciate your time, expertise, and thoughtful contributions to today’s discussion.
