Whitepaper: Mitigating Risks in Oligonucleotide Therapeutic Development, Unlocking the Power of Sensitivity and Selectivity

Oligonucleotide therapies, including small interfering RNA (siRNA), microRNA (miRNA), and inhibitory antisense oligonucleotides (ASOs), have emerged as a promising group of molecules for gene inhibition (Hu et al., 2020). These therapies hold particular potential in addressing rare diseases that lack cost-effective conventional treatments. Oligonucleotides, also known as RNA interference (RNAi) therapies, are also actively being researched in various fields, including oncology, infectious diseases, neurological disorders, hepatic conditions, and ophthalmology. Amongst these therapies, siRNAs are the most extensively researched modality, followed by miRNA and ASOs. While siRNA therapies have made notable progress in reaching the market, the overall number of FDA approved oligonucleotide therapies remains limited, around 3% (figure 1).  This is primarily due to regulatory authorities facing challenges in updating their criteria to account for the unique characteristics of these therapies, leading to prolonged delays. Other significant challenges include development, manufacturing and ensuring product stability. Consequently, the majority, approximately 97%, of potential oligonucleotide therapeutics are currently in various stages of development, including discovery, preclinical, or clinical testing. Sensitivity and selectivity play a pivotal role in oligonucleotide therapeutic development, contributing to the successful translation of these therapies from the laboratory to the clinic. Sensitivity refers to the ability to accurately detect and quantify oligonucleotides at low concentrations, which is essential for assessing their efficacy and identifying potential toxic effects. To optimize transfection and reduce off-target effects, oligonucleotide therapies are typically administered in very low doses. For example, efficient gene knockdown has been achieved with intracellular amounts of less than 2000 siRNAs per cell, even down to picomolar concentrations. Additionally, oligonucleotides are quite small, with siRNAs typically ranging from 19 to 29 nucleotides in length. Short siRNAs are often preferred to avoid provoking an inflammatory antiviral immune response, which can occur with longer siRNAs. Such low dosages and short molecular lengths pose significant analytical challenges in oligonucleotide development and safety testing.  Selectivity, on the other hand, involves the ability to distinguish the target oligonucleotide from other molecules present in complex biological matrices, minimizing the risk of false-positive or false-negative results. The primary safety concern for oligonucleotides revolves around the possibility of hybridization-dependent effects, also called off-target effects, which can be caused by inadvertent binding of the oligonucleotide to unintended RNAs that have a sequence similar to the target RNA. Sequence specificity, in this context, relates to an oligonucleotide’s ability to differentiate its intended target RNA sequence from all other RNA molecules within the cell. It’s important to note that both ASOs (antisense oligonucleotides) and siRNAs (small interfering RNAs), while employing different mechanisms, can trigger off-target effects through hybridization. Achieving high sensitivity and selectivity ensures accurate measurement of oligonucleotide concentrations, reduces ambiguity in outcomes, and enhances the overall safety profile of the therapeutic. This whitepaper emphasizes the growing need for sensitive and accurate quantification methods to support the development of oligonucleotide drugs. As 97% of potential therapeutics are still in the discovery, preclinical, or clinical testing phase, it is crucial for pharmaceutical developers to secure lab partners with capabilities to support oligonucleotide analysis.  While larger organizations may have more experience in this field, collaborating with them can often feel alienating, with limited transparency in the results. Sannova, on the other hand, stands out as one of the few boutique CROs that not only offers oligonucleotide expertise but also provides a friendly, transparent, and personalized experience. Our expertise in overcoming PK and TK analysis challenges guarantees the reliability and quality of the data, supporting the safe and effective progression of your preclinical oligonucleotide therapeutics towards clinical applications. With over 15 years of experience, our lab caters to the multi-billion dollar market for bioanalytical and CMC services. Headquartered in Somerset, NJ, our midsize team of dedicated professionals has successfully completed over 1,300 bioanalytical and over 1,000 CMC projects for a diverse range of clients. We are committed to maintaining exceptional quality and continuously optimizing our processes, allowing us to develop cost-effective, customized solutions within short time frames. Visit our website to explore how our bioanalytical and CMC services can support your innovations.

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