Targeted RNA degradation

Targeted RNA degradation: Principle and Therapeutic Promises

RNA, or RiboNucleic Acid, is a structured macromolecule which plays a central role in numerous cellular functions. If less than 3% of RNA transcripts get translated into proteins, the large majority of the human genome is transcribed in non-coding RNAs (ncRNAs), directly involved in essential biological processes such as regulating protein production and gene expression. As a result, many diseases, such as neurological disorders, diabetes, cardiological and cancer diseases, are linked to RNAs because cells rely on the correct expression of both coding and non-coding RNAs to function. RNAs are commonly targeted with antisense oligonucleotide-based modalities (ASOs) with success in the clinic and FDA approved medicines¹.

However, low cell membrane penetration, physiological side effects along with activation of the immune response are limiting the use of ASO. More importantly, ASO are best known to bind to unstructured regions of RNA. Since the majority of RNA targets are structured, ASO strategy has limitation, making the 3D structure regions of the RNA a valuable drug target accessible for small molecules. If binding RNAs with small molecules is currently intensively investigated by many companies (PTC Tx, Arrakis Tx, ReviR Tx, Etc…), other ways for destabilizing or metabolizing RNAs have recently emerged. A promising new technology is attracting more attention: converting an RNA-binding small molecule into an RNA degrader.

Ribotac, the hope to target the undruggable?

In 2018, Disney’s group reported the first targeted RNA degraders, called RIBOTACs or ribonuclease-targeting chimeras, by inducing proximity between the targeted RNA, microRNA-96, upregulated in cancer cells, and a ribonuclease (RNAse), an endogenous nuclease that naturally regulate RNA lifetime.² The authors succeeded to degrade selectively the target in vitro as well as in vivo in a mouse model of breast cancer metastasis.

By analogy with PROTACs (proteolysis targeting chimeras) that target and degrade proteins, RIBOTACs are heterobifunctional small molecules with two specific warheads: one is able to bind selectively to RNA, the second one recruits then activates RNAse L. The newly formed complex triggers RNA degradation.

Short after its discovery, this technology has been successfully applied to others oncogenic RNAs, such as JUN and MYC, targets long considered to be undruggable and overexpressed in more than 20 different cancer types.³ Those RIBOTAC degraders, synthesized from silent binders, potently degraded the desired targets and therefore downregulated the disease-causing RNA. Besides, Duca’s group applied this interesting approach to tackle SARS-CoV 2 by conjugating a RNA binder, Covidcil-19, to a heterocyclic recruiter of RNAse L.⁴ The newly formed Covidcil RIBOTAC compound showed the ability to induce targeted cleavage and degradation of the entire SARS-CoV construct.

This new chemical modality that explores innovative mechanisms of action, offers exciting perspectives for the understanding of RNA biology and targets function. However, a lot of pitfalls remains for the development of future drugs. The metabolic stability of such high molecular weight molecules is obviously a concern along with Beyond Rule of 5 properties, even though advanced PROTACs in clinics tempt to prove it is possible. In addition, the development of a highly specific ligand seems to be crucial since degraders can in theory destroy anything they bind and per se bring unexpected toxicity.

Finally, we can ask ourselves about the critical role of the RNAse L, not evenly expressed across different tissues. If RIBOTACs depend on its endogenous concentrations, not all cell types would be compatible with this approach. To face this problematic, developing more potent RNAse L activators and new small molecules recruiters capable of activating other ribonucleases might bring a part of the answer.

Combining forces to develop mRNA-targeted small molecule drugs

Recently, Oncodesign Services and Veritas In Silico entered into a business cooperation on developing a specific offer related to mRNA-targeted small molecule drugs. Veritas in silico can rapidly identify novel hits with its proprietary drug discovery platform, ibVIS®, consisting of computational target identification of any given mRNA along with robust and quantitative high throughput screening.

Oncodesign Services offers integrated drug discovery services from the conception and design of molecules, through efficient and intelligent optimization and evaluation, to sustain preclinical candidate selection and nomination. We successfully applied a proprietary targeted protein degrader’s platform to the discovery of novel Protacs on behalf of clients. This platform includes the design and synthesis of linkers/E3 Ligase binders’ libraries. The implementation of supporting degradation assays (Nano-Glo® HiBiT detection system and Automated western blotting) along with biophysical characterization (Evaluation of binary and ternary complex formation, MST, GCI, Nano DSF) enble a rapid turnaround for proof of concept. A similar platform is currently implemented for RNA degradation.

The combination of these two platforms from Oncodesign Services and Veritas In Silico may contribute to the discovery of novel mRNA binders and to mRNA degraders. Please get in touch if you are interested to hear more about how this collaboration could benefit to your drug discovery programs.

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About the authors

This blog post was written by Christophe Parsy, head of medicinal chemistry & Aurélien Tap, senior medicinal chemist at Oncodesign Services. In their current role, they work to accelerate drug discovery programs from target identification through to IND.

References:

1. Stein CA, Castanotto D. 2017. Mol Ther. 2017;25(5):1069–1075.
2. M. D. Disney et al. J. Am. Chem. Soc. 2018, 140, 6741-6744
3. M. D. Disney et al. Nature2023, 618, 169–179.
4. M. Duca et al. ACS Cent. Sci.2020, 6, 1647-1650