Smarter DMPK Strategies for Preclinical Oligonucleotide Development: Accelerate Progress & Enhance Safety

Oligonucleotide (oligo) therapies are gaining momentum due to their broad applications in diagnostics, therapeutics, research, and personalized medicine. These treatments offer precise, sequence-driven targeting, spanning rare genetic diseases, oncology, and neurology. They are also often effective in low doses and have the potential to be developed more quickly than traditional drugs. 

However, oligos differ significantly from conventional therapies in how they are absorbed, distributed, metabolized, and excreted (ADME). As their use expands, oligos’ unique biological properties necessitate a new approach to drug metabolism and pharmacokinetics (DMPK) based on platform strategies and supported by in vitro models.

Why DMPK Matters for Oligos

Understanding the DMPK characteristics of a drug is critical for predicting its safety, efficacy, and appropriate dosing. This process is particularly challenging for oligos because they are administered systemically. Compared to traditional therapies, oligos also tend to:  

• Be poorly absorbed orally and require injection.
• Exhibit high tissue accumulation in the liver, kidneys, and spleen.
• Undergo degradation into short, sometimes active, fragments.
• Rely on renal clearance, which can vary based on tissue binding and chemical modification.

These characteristics make understanding oligos’ DMPK processes more complex yet essential to safe, scalable pathways to regulatory compliance.

Oligos’ Distinct Pharmacokinetic Profile 

Oligos occupy a unique space in drug development: they are larger than small molecules but smaller than protein-based biologics. Oligos also have a high negative charge and are hydrophilic, making crossing lipid-rich cell membranes or the highly regulated blood-brain barrier (BBB) especially difficult. These characteristics create distinct challenges that complicate oligos’ delivery to target areas.

Oligos typically accumulate in the liver, kidneys, spleen, lymph nodes, adipose tissue, and bone marrow. This distribution pattern raises questions about off-target toxicity and reduced clearance, highlighting the importance of delivery strategies and chemical modifications.  Additional challenges include:

1. Stability: Oligos break down quickly in the body unless they are chemically modified for protection.
2. Metabolism: Unlike small molecules, which are metabolized mainly by liver enzymes, oligos are broken down into smaller fragments. Some may remain active, raising toxicity questions.
3. Excretion: They are typically cleared by the kidneys, but clearance can be reduced or delayed depending on their route of administration and tissue binding. 
4. Bioavailability: Oligos cannot be taken orally due to their susceptibility to degradation in the gastrointestinal tract and their poor absorption, so they are delivered by intravenous, subcutaneous, or intrathecal injection, adding complexity to the patient experience and study design.

CNS Delivery

Perhaps the most technically challenging frontier in oligo therapy is central nervous system (CNS) delivery. The BBB is a formidable obstacle that excludes almost all large (>600 Da) and hydrophilic molecules, and direct CNS delivery is often required. Intrathecal lumbar (IT-L) injection is the most common approach to bypassing the BBB, but it is procedurally difficult, risks failed exposure to the target site and is susceptible to patients’ anatomical differences.

To address these challenges, researchers have developed dual-catheter surgery models that allow administration through the lumbar spine and sample collection from the cisterna magna, located near the base of the skull, which helps cushion the brain and the spinal cord.

This approach improves success rates, enables repeated cerebrospinal fluid (CSF) sampling without additional anesthesia, and enhances understanding of drug exposure within CNS tissues. These advances are pivotal for expanding the reach of oligo therapies into neurology and neurodegenerative disease.

The Case for In Vitro Strategies

To better predict oligos’ in vivo efficacy, toxicity, and off-target behavior, scientists are increasingly turning to platform-based DMPK strategies and specialized in vitro models. Specifically, advanced assays and 2D/3D cell cultures enable early identification of active drug fragments and support more efficient, safer development. For CNS-targeted oligos, dual-catheter intrathecal systems improve access to hard-to-reach areas such as the brain and spine, helping mitigate risk and accelerate development timelines. These advancements help illustrate the full therapeutic potential of oligo-based treatments.

Metabolism models represent another in vitro strategy that can help predict how an oligo will behave in the body and inform key decisions about dosing, toxicity, and formulation. Common in vitro models include:

• Plasma and Serum Stability: Used to assess compound stability before cellular entry. Results can vary depending on the anticoagulants used and fresh or frozen plasma use.
• Liver Homogenate, S9, and Lysosome Models: Provide insights into tissue-specific metabolism, particularly for liver-targeted oligos.
• Lysosomal Incubation: Mimic the acidic, enzyme-rich environment of intracellular compartments like endosomes and lysosomes, helping researchers anticipate intracellular breakdown pathways.

Validation studies show these models demonstrate strong in vitro–in vivo correlation (IVIVC), supporting their use in early-phase screening and regulatory submissions.

Why Metabolite Monitoring Matters

Careful metabolite monitoring is essential because oligo metabolites can remain biologically active. Both sense and antisense strands may degrade at different rates, and even minor metabolites can influence therapeutic outcomes or safety. 

Researchers frequently combine liquid chromatography-tandem mass spectrometry (LC-MS/MS) and quantitative PCR (qPCR) to monitor these changes. LC-MS/MS offers high sensitivity and precision for identifying and quantifying oligo fragments, making it particularly useful for characterizing degradation patterns. In contrast, qPCR is effective for tracking specific sequences, though it provides less information about the nature of degradation products. While each method has its limitations, together they offer a more complete picture of oligonucleotide metabolism and clearance.

As oligos become more popular and better understood, success will depend on scientists’ abilities to adapt drug development platforms and strategies to fit their unique properties. Platform-based DMPK strategies and specialized in vitro models are essential for reducing risk, improving predictability, and maintaining development timelines. Innovations in delivery further expand oligos’ potential in areas like neurodegenerative diseases.

By investing in more innovative DMPK strategies, drug developers and sponsors can reduce late-stage failures and bring safer, more effective oligo therapies to patients.

Yan Pan, Ph.D., is a group leader in the DMPK Study Director Team at WuXi AppTec’s Shanghai site. He has over fifteen years of experience in drug metabolism and pharmacokinetics.