Oligonucleotide Discovery

PRISMTM is Wave Life Sciences’ proprietary discovery and drug development platform that enables us to target genetically defined diseases with stereopure oligonucleotides across multiple therapeutic mechanisms. We are using PRISM to develop optimized, stereopure oligonucleotides as potential treatments for inherited retinal diseases, including Usher syndrome and retinitis pigmentosa. We present preclinical data demonstrating that these oligonucleotides have potent and durable activity in cellular, ex vivo, and animal models.

While siRNA mediated gene silencing can inhibit the growth of cancer cells in vitro, many siRNA therapeutics have failed to progress since silencing a single target did not have a broad enough inhibitory effect. It is often important to inhibit multiple targets within a specific cancer type – to improve efficacy and/or broaden utility of the treatment. Delivery of multiple siRNAs within a tumor can benefit from potential synergies in the genes being silenced or by improving effects of existing therapeutics. Sirnaomics has developed Polypeptide NanoParticles (PNPs) that can deliver more than one siRNA into the same cell concomitantly. We have demonstrated the ability for our siRNAs to augment activity of existing therapies – including Immune Checkpoint Inhibitor antibodies and small molecule therapies with dramatic results. This presentation will present the latest data on these products.

Wave Life Sciences’ proprietary discovery and drug development platform PRISMTM enables the precise design, optimization and production of stereopure oligonucleotides for genetically defined diseases. PRISM combines our unique ability to construct stereopure oligonucleotides with a deep knowledge of how the interplay among oligonucleotide sequence, chemistry and backbone stereochemistry impacts key pharmacologic properties. Our current focus for clinical development is in neurology. We are conducting two clinical trials in Huntington’s disease (HD), advancing additional HD programs, as well as targeting C9ORF72 in amyotrophic lateral sclerosis and frontotemporal dementia. We are also advancing discovery research in inherited retinal diseases and hepatic diseases.

A subset of GalNAc-siRNAs does not pass nonclinical safety evaluation due to hepatotoxicity that can be largely attributed to RISC-mediated off-target events. To minimize these events, we developed a novel design strategy, termed ESC+, which utilizes chemical modifications that thermally destabilize base pairing between the seed region of the guide strand and off-target RNAs, resulting in an improved nonclinical safety profile and favorable translation in humans.

Oligonucleotide therapeutics such as ASOs and siRNAs may elicit undesirable side effects through a variety of off-target mechanisms. Combining in silico searches with RNA sequencing offers a powerful platform for detecting off-target events and selecting the most suitable oligonucleotides for successful drug development.

Oligonucleotide manufacture is well known for possessing poor green chemistry metrics, and consequently there have been many efforts across the industry to improve the situation. This presentation will summarise an ACS Pharma Round Table perspectives article on the sustainability of oligonucleotide manufacture due for publication in 2020, and will include an assessment of the sustainability of the current state of the art for oligonucleotide manufacture, and efforts being made in the community to improve the situation

Most commercial dyes contain large hydrophobic and/or polar groups that may affect the uptake, release, trafficking and accumulation of the oligo in cells. We have developed so-called stealth labels to ensure that imaging data stay closer to the true events in the cells. One technique is based on isotope labels while a second technique is based on fluorescent base analogs. The pros and cons of these techniques will be disclosed during the presentation.

The VECTrans® technology is based on molecular vectors, including camelid-derived VHH nanobodies, that target specific endocytic receptors expressed at the blood-brain barrier or in specific peripheral organs or tumours and promotes the intracellular delivery of therapeutic drugs. We have applied this technology to the delivery of nucleic acids and demonstrate the efficient targeting and gene silencing, at therapeutic doses, of TfR-targeted VHH-siRNA bioconjugates in extra-hepatic organs.

MicroRNAs are short non-coding RNAs that regulate biochemical pathways and networks of pathways by the mechanism of RNA interference (RNAi). MicroRNA-21 has been implicated in multiple organs as a microRNA associated with fibrotic diseases and cancer. We have generated an anti-fibrotic microRNA-based therapeutic approach by targeting microRNA-21 with an antisense oligonucleotide (anti-miR-21). This microRNA-based drug is now in a phase 2 clinical trial for a fibrotic kidney disease called Alport Syndrome.

Silence Therapeutics explores different options for fine tuning of GalNAc-conjugated siRNA design. Areas of special interest include siRNA modification patterns, end stabilisation, linker chemistry, and the number and location of GalNAc units. We also explore if GalNAc conjugate design/synthesis principles will be useful when designing siRNA conjugates for extra-hepatic purposes.

Inability to selectively deliver antisense oligonucleotide (ASO) therapies to extrahepatic tissues is a substantial barrier to the development of treatments for extrahepatic tissue specific diseases. We evaluated several G protein-coupled receptors for targeted delivery of ASOs. Our results show that the G protein coupled receptors such as GLP1, angiotensin and sortilin receptors, among others can be used for improving productive uptake of ASOs in cells and in animals. A summary of our findings will be discussed.

Antisense based therapeutics uses short chemically modified oligonucleotides (ASOs) to bind complementary mRNA via Watson-Crick base-pairing and modulate RNA function to produce a pharmacological effect. There are currently over 40 ASO drugs in clinical trials and medicinal chemistry played critical role in achieving these milestones. Over the years Ionis have developed numerous chemical approaches to improve affinity, metabolic stability and protein binding properties of ASOs. The chemical modifications also resulted in an increase in tissue half-life enough to support monthly or less-frequent dosing, and substantial improvements in safety and tolerability. Recently, targeted delivery enhanced ASO delivery to tissues and cells of interest and this approach demonstrated significantly improved activity and tolerability. An overview of Ionis chemical approaches for improving the properties of ASO drugs will be presented.

Gene therapy has greatly expanded to become a standard therapeutic option in addition to small molecules and protein therapeutics. The use of synthetic oligonucleotides (ONs) to abolish, restore, or correct a nucleic acid target depends on both the type of ON cargo and the desired target. Another complexity is delivery, which may be improved by conjugating or complexing the ON cargo with vectors for enhanced efficiency. Our research interests can be divided into two areas: 1) Investigations of ON chemistries, based mainly on Locked Nucleic Acids (LNA), which allow effective targeting of DNA (anti-gene ON) in triplet-repeat disorders and 2) Optimizing non-viral delivery vectors (peptide dendrimers) for efficient and safe delivery of splice-switching ONs.

This presentation will discuss how variants of LNA-based antisense oligonucleotides, eg. lipophilic cationic variants, can be explored as building blocks towards optimizeing plasma half-life, biodistribution and gene knock-down. Importantly, the Lipo-LNA antisense technology offers the opportunity of using phosphorodiester instead of phosphorothioate linkages.