Daniel Pfeffer, Director of Oligonucleotide Production at Bachem shares why CDMO innovation is key to advancing next-generation oligonucleotide therapies.
Bachem
Oligonucleotides are continuing to transform modern medicine, with unique properties allowing targeted therapies to treat rare conditions. Their ability to modulate gene expression make them a versatile and groundbreaking treatment option, with minimal side effects. This precision makes oligonucleotides a promising option for conditions that have previously been difficult to treat, ranging from cardiovascular disorders to central nervous system diseases.
The oligonucleotide therapeutic market is expanding rapidly. More than 20 synthetic oligonucleotides have been approved, and more than 700 are in development. Key classes include antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and RNA aptamers.
ASOs selectively bind RNA to regulate gene expression, siRNAs degrade target mRNA via RNA-induced silencing complexes, and RNA aptamers fold into unique three-dimensional structures to bind molecular targets with high specificity. Such specificity allows therapies to be rationally tailored to disease-associated molecular targets, with the potential for improved treatment precision and effectiveness.
Despite their promise, the development of oligonucleotides bears certain challenges. Limitations include:
1. Stability and half-life
- Prone to degradation by nucleases
- Can be rapidly cleared by liver and kidneys requiring frequent dosing
2. Tolerability
Immunogenicity
3. Cellular uptake
Often inefficient with poor endosomal escape
4. Tissue targeting
- Insufficient target specificity or enrichment in non-target tissues
- Crossing of biological barriers
One of the most successful strategies to overcome these challenges is to use conjugation chemistry, which links oligonucleotides to peptides, antibodies, carbohydrates, or other moieties. Conjugation can improve stability, enhance cellular uptake, and direct therapies to specific tissues, making these drugs more clinically viable.
Using peptides to improve oligonucleotide delivery
Peptides are particularly effective molecules for conjugation due to their specificity, safety profiles, and versatility. In conjugation, peptide–oligonucleotide conjugates (POCs) make use of peptides’ targeting capabilities to improve the therapeutic delivery of oligonucleotides.
Cell-penetrating peptides (CPPs) and receptor-targeting peptides are some of the approaches that can be used. CPPs are short, often positively charged sequences that facilitate cellular entry and endosomal escape, ensuring the oligonucleotide reaches its target. Receptor-targeting peptides bind receptors overexpressed in specific tissues, improving selectivity and reducing systemic side effects.
Examples of POCs include cRGD–siRNA conjugates, which target αvβ3 integrin receptors to improve tumor uptake, and GLP1R–ASO conjugates, which deliver oligonucleotides specifically to pancreatic β-cells for targeted gene silencing. These conjugates illustrate how targeted peptide-mediated delivery can enhance tissue-specific gene silencing in preclinical models.
Choosing the right conjugation strategy for therapeutic success
Manufacturers have several chemistries at their disposal, and selecting the appropriate method is critical. Common strategies include:
- Thiol–maleimide reactions: Form stable thioether bonds, often used to link CPPs to siRNAs.
- Disulfide linkages: Reversible under cellular conditions, allowing intracellular release.
- Click chemistry: Copper-catalyzed (CuAAC) and copper-free (SPAAC) azide–alkyne cycloadditions provide modular, high-yield, bioorthogonal conjugation options.
- Oxime, thiazolidine, and hydrazone bonds: Mild reactions that maintain oligonucleotide stability.
- Amide bond formation: Simple and robust, suitable for a wide range of peptide conjugates.
Choosing the right chemistry depends on the properties of the oligonucleotide and ligand, the intended tissue, cellular target, and the desired in vivo stability, and is crucial for achieving efficient therapeutic delivery.
Improving patient outcomes through conjugation chemistry
Through conjugation chemistry, delivery of can be made more efficient and tissue-selective, allowing manufacturers to meet rising demand and accelerate access to medicines.
Targeted delivery strategies increase the proportion of oligonucleotides reaching intended cells, which can enhance on-target activity while reducing exposure in non-target tissues and the risk of off-target effects. In some cases, such as GalNAc–siRNA conjugates targeting hepatocytes, improved delivery has enabled lower and less frequent dosing, with associated benefits for tolerability and convenience. Conjugation approaches are also expanding the range of tissues that can be addressed, offering potential therapies for organs that were previously difficult to reach.
For example, cRGD–siRNA conjugates have demonstrated significant tumor volume reduction, and GLP1R–ASO conjugates have demonstrated improved gene silencing in pancreatic β-cells, illustrating how precise delivery benefits patients clinically.
Manufacturing considerations
Producing peptide–oligonucleotide conjugates requires specialist expertise in both peptide and oligonucleotide chemistry. Solid-phase synthesis is well-suited for shorter constructs, allowing the conjugate to be built in a single sequence with fewer purification steps. Post-synthetic conjugation, on the other hand, is used to attach longer peptides or full proteins to oligonucleotides. Both approaches can be scaled for GMP production, facilitating the translation of research findings into clinically viable therapies.
Advancing therapies with TIDE innovation
Conjugation chemistry is a key strategy to overcoming the delivery challenges of oligonucleotide therapeutics. By carefully selecting conjugation parameters, CDMOs can support their customers in improving cellular uptake, tissue specificity, and stability of their molecules, resulting in more effective therapies. Ultimately, these strategies translate into better patient outcomes and expanded clinical impact, helping bring next-generation oligonucleotide treatments to patients more efficiently.