FDA guidances for development of oligonucleotide therapeutics: Key takeaways for sponsors

This blog is part of The Regulatory Navigator series, where we explore the evolving regulatory landscape with actionable insight from Parexel's experts, sharing their experience to maximize success for clinical development and patient access.

Published May 5, 2025 

Background

Oligonucleotide therapeutics (ONTs) are an emerging class of therapeutics. Invaluable for addressing several genetic diseases, they hold the promise of reshaping disease progression through precise and targeted interventions.¹ With increasing numbers of ONTs in development, the FDA has approved 17 products² to date. 

ONTs have unique chemical characteristics that influence their physiologic effects. From a biochemical standpoint, ONTs are either short single-stranded synthetic RNA or DNA molecules (antisense oligonucleotides, ASO), whereas double-stranded RNA nucleotide sequences are called small interfering RNA (siRNA). ONTs bind to complementary nucleic acid sequences as targets to alter RNA and protein expression. ONTs share some aspects of small molecules (e.g., molecule size, renal filtration) and biologics (unique metabolic pathways in tissues), but are not classified as either. ONTs are usually chemically modified (such as backbone modification and conjugation) to prolong their half-life.³ Also, the route of administration (e.g. local or systemic) determines the exposure.

The FDA released two guidances in 2024 to address specific considerations for the development and assessment of ONTs from non-clinical and clinical pharmacology perspectives: 

1. Draft guidance on Nonclinical Safety Assessment of Oligonucleotide-Based Therapeutics⁴ 
2. Final guidance on Clinical Pharmacology Considerations for the Development of Oligonucleotide Therapeutics⁵ 

In this blog, we share our recommendations for ONT product development aligned with the key focus areas of these guidances. 

Nonclinical safety considerations

Previously, the FDA’s non-clinical requirements for ONT products were similar to those of small molecules. However, the current draft guidance describes amended recommendations for nonclinical assessment of ONTs. Of note, immune stimulatory oligonucleotides and CBER-regulated products (DNA/RNA vaccines, virally delivered ONTs, messenger RNA and RNA used for gene editing) are excluded from the scope of the guidance.

ONT-specific pharmacology studies 

The draft guidance provides several recommendations for pharmacological assessment of ONTs that are distinct from those outlined in the ICH M3(R2) guideline.⁶ The recommendations are closely related to those for cell and gene therapy (CGT) products, which is not surprising given the analogous mechanisms of action of ONTs and CGTs. Specifically, the risk for exaggerated on-target effects and off-target hybridization dependent and independent effects should be examined for ONT products. 

An in vivo assessment of the potential for adverse effects that result from exaggerated pharmacology is recommended, and the use of test-species active surrogate oligonucleotides for this purpose is encouraged. Although pharmacologically relevant species should be used, if none are available (as defined in the guidance), in vivo assessment should still be conducted to assess off-target effects. As ONTs are designed to act through binding to nucleic acids, the ability of the product to bind to non-targeted RNA or DNA sequences that share complementarity with the ONT base sequence and the sequence of any predicted metabolites should also be conducted. This should be done using appropriate in silico or in vitro methods and followed by an in-vitro follow-up study of any significant hits. Potential hybridization to the transcriptome and nuclear and mitochondrial genome should also be evaluated. 

The draft guidance also recommends that potential off-target, hybridization-independent events should be evaluated. ONTs have the potential to interact directly with proteins or other cellular components in a sequence-dependent manner. Testing for non-hybridization dependent effects can be done in the IND-enabling toxicology studies, as discussed next.

Safety assessments unique to ONTs

For ONT products, a toxicology program that is consistent with the ICH M3(R2) guideline⁶ is advised – with toxicology studies conducted in one rodent and one non-rodent species. Though at least one species should be pharmacologically relevant, toxicology studies in two species are recommended even if one (either rodent or non-rodent) or both (rodent and non-rodent) species is not pharmacologically relevant. In our recent experience, when sponsors with early-stage ONT programs have asked the FDA for agreement on toxicology programs, the FDA has declined to agree that a single species is sufficient to support IND initiation.

Off-target, hybridization-independent events can still be evaluated without expression of the relevant DNA or RNA target. 

Since the use of animal surrogate ONT products is encouraged, sponsors should include groups treated with both the clinical candidate and the surrogate to assess both exaggerated pharmacology and non-hybridization dependent effects. 

Regarding other safety assessments, hERG studies can be omitted for ONTs belonging to a well-characterized class that has not demonstrated ability to inhibit the ion channel. Genotoxicity testing is generally not considered to be necessary either, but for those ONTs warranting an empirical assessment of genotoxicity, the test batteries recommended in ICH S2(R1)⁷ are generally considered appropriate. 

For reproductive and developmental toxicity, where the weight-of-evidence from existing data can indicate an obvious adverse effect of an ONT on fertility or pregnancy outcome, these data may provide adequate information to communicate the risk to reproduction and embryofetal development, and no additional nonclinical studies are warranted. 

Finally, for ONTs that are members of a class that have been well characterized for carcinogenicity risk, it can be appropriate to conduct a two-year carcinogenicity study in a single species. In any case, the ICH S1A⁸, S1B(R1)⁹ and S1C(R2)¹⁰ and M3(R2)⁶ guidelines should be followed by sponsors to define the need and timing of these studies.

FDA allows an abbreviated nonclinical package for nano rare diseases (n of few)

Of special interest to those developing drugs for nano rare diseases is the FDA’s flexibility regarding requirements for nonclinical data.  Sponsors can leverage a series of guidances specific to antisense ONT products that allow for a substantially abbreviated nonclinical package to support IND initiation. The FDA’s flexibility was initially described in its previously issued draft guidance, Nonclinical Testing of Individualized Antisense Oligonucleotide Drug Products for Severely Debilitating or Life-Threatening Diseases Guidance for Sponsor-Investigators (2021).¹¹ 

The 2021 and 2024 nonclinical ONT guidances allow for a pharmacology package that includes convincing proof-of-concept studies and a single in silico evaluation of hybridization-dependent off-target binding. Crucially, while safety pharmacology endpoints as outlined in the ICH S7A guideline are still recommended, in vitro hERG testing is not warranted, and toxicology may be limited to a well-designed, three-month GLP-compliant study in a single species. Genotoxicity assessment is also not warranted.

It is important to note that to leverage these guidances, the investigational antisense ONT must be from a well-characterized class of ONTs. While the FDA does not specifically define “well-characterized,” in practice Parexel has found this to mean that there is substantial data regarding the toxicity of antisense ONT in long-term toxicology studies in rodent and non-rodent species, with a focus on non-human primate studies of at least 13-weeks duration.

Clinical pharmacology considerations

Critical clinical pharmacology items for each drug development program are:

• An assessment of the potential for electrophysiological changes (i.e. QTc interval prolongation) 
• Proarrhythmic potential 
• The immunogenicity risk 
• The impact of hepatic and renal impairment on dosing recommendations and safety 
• Assessment of the potential for drug-drug interactions (DDI)

Sponsors are advised to conduct pharmacokinetic analysis on ONTs after both single and multiple doses (which is typical during early stages of drug development). However, the challenge with this drug class is that systemic pharmacokinetics might not accurately represent the distribution in the target tissues, nor a correlation to the pharmacodynamics, safety, or efficacy. These drugs distribute and accumulate in tissues and have long pharmacodynamic half-lives, leading to sustained pharmacodynamic responses. Therefore, in multiple-dose studies, sponsors should incorporate an evaluation of appropriate pharmacodynamic biomarkers, such as target mRNA, target protein, or downstream biomarkers that reflect the modulation of the target protein. 

QTc prolongation potential assessment 

Regulators do require an assessment of the QTc prolongation potential for ONTs. In the recent guidance, the FDA states that to date, no large mean effect of ONTs on the QTc interval has been observed in the small number of dedicated QT studies reviewed. While dedicated QT studies (“thorough QT” studies) can be large and require a significant budget, we recommend using alternative methods such as concentration-QT analysis, which must be prospectively planned in early clinical trials (such as single and multiple ascending dose studies). In the future, with a growing body of evidence, the requirement for dedicated QT studies may be waived in well-characterized class of ONTs.  As described above, in vitro hERG testing is not warranted in a well-characterized class of ONTs.

Immunogenicity risk for ONTs

As stated in the guidance, an unwanted immune response to an ONT can be generated to the carrier, backbone, oligonucleotide sequence, or any novel epitopes created from the whole drug (carrier plus oligonucleotide) or even a modified protein as a result of the interference. In case the ONT generates a modified protein, the sponsor should consider an immunogenicity assay measuring antibodies to the modified protein. The immunogenicity risk depends on the product characteristics itself, on the pharmacology, and on patient factors. 

For example, a product that is given frequently via the subcutaneous route and has a large carrier, such as polyethylene glycol (PEG), may bear a higher risk of immunogenic reaction than a product without these features. 

We advise sponsors to evaluate the potential for immunogenicity in the general toxicology studies (assessment of ONT-induced effects on the release of cytokines, activation of the complement system, production of antidrug antibodies, etc.). As emphasized in the guidance sampling strategies should align between PK and PD assessments and evaluate any impact of anti-drug antibodies (ADA) on those. As usually done for any potentially immunogenic product the immunogenicity assessment includes a multi-tiered assay approach (similar to biologics) and with a sampling strategy over the entire development program. Although not explicitly mentioned in this guidance it is expected by the regulators that an integrated summary of immunogenicity is filed within the drug marketing authorization application to address the risk. We have helped numerous sponsors in adequate clinical study design, sampling strategy, clinical immunogenicity data analysis as well as with the creation of integrated summary reports. 

Clinical trials with ONTs in special populations and drug-drug interaction studies 

Collecting data from patients with hepatic or renal impairment is important as these groups may be exposed to increased risk for side effects and such information is required to answer regulatory questions. FDA encourages sponsors to enroll participants with a full range of hepatic and/or renal function in the late-phase trials, if the drug is not predominantly renally cleared or does not target the liver. Sponsors should use preclinical, PK, PD, safety, and tolerability information from early clinical trials to assess the risk. 

At Parexel, our experience is that not including those populations in late-phase clinical trials requires justification and can lead to requests from the agency or label restrictions. We recommend that sponsors should use state-of-the-art modeling techniques (e.g., population PK-PD modeling), if feasible, to investigate the relationship.

Given their metabolic fate and PK behavior, DDIs based on PK assessments play a minor role in ONTs and generally are not required; however, the guidance points out that, based on the mechanism of action, a pharmacodynamic interaction may become relevant and require further assessment.

Key takeaways and next steps for sponsors developing ONTs 

ONTs have some unique characteristics compared to small molecules or biological products and require a tailored approach in the non-clinical and clinical setting:

Parexel offers specific ONT-tailored consulting services, with a proven track record of working with sponsors to achieve positive regulatory outcomes for these medicinal products. We recommend that sponsors consult with FDA during the development process if alternative approaches are to be justified. Parexel’s experts can support that consultation and advise on ways to optimize your ONT drug development program.

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References:

1. Collotta D, Bertocchi I, Chiapello E, Collino M. Antisense oligonucleotides: a novel Frontier in pharmacological strategy. Front Pharmacol. 2023 Nov 17;14:1304342. 
2. Guidance Recap Podcast: Clinical Pharmacology Considerations for the Development of Oligonucleotide Therapeutics. FDA, June 2024. 
3. Edvard Smith C. I., Zain R. (2019). Therapeutic oligonucleotides: state of the art. Annu. Rev. Pharmacol. Toxicol. 59, 605–630. 10.1146/annurev-pharmtox-010818-021050
4. Nonclinical Safety Assessment of Oligonucleotide-Based Therapeutics. FDA, November 2024. 
5. Clinical Pharmacology Considerations for the Development of Oligonucleotide Therapeutics. FDA, June 2024. 
6. ICH M3(R2) Guidance on Nonclinical Safety Studies for the Conduct of Human Clinical Trials and Marketing Authorization for Pharmaceuticals, June 2009
7. ICH guideline S2 (R1) on genotoxicity testing and data interpretation for pharmaceuticals intended for human use
8. ICH Topic S1A, The Need for Carcinogenicity Studies of Pharmaceuticals
9. ICH guideline S1B(R1) on testing for carcinogenicity of pharmaceuticals
10. ICH S1C (R2) Dose selection for carcinogenicity studies of pharmaceuticals - Scientific guideline
11. Nonclinical Testing of Individualized Antisense Oligonucleotide Drug Products for Severely Debilitating or Life-Threatening Diseases Guidance for Sponsor-Investigator, April 2021. 
     

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