Ribonucleic acid (RNA) plays a critical role in cellular diversity and gene expression and may offer more drug targets than proteins. However, due to their small size and relatively poor stability, RNA molecules have long been considered “undruggable” targets. Currently, strategies targeting RNA primarily include RNA interference (RNAi) and antisense oligonucleotides (ASOs). These approaches can bind target RNA with high specificity, but their large molecular size poses challenges for intracellular delivery. In contrast, small-molecule drugs more easily penetrate cell membranes and bind to RNA. If nucleases can be recruited near RNA to achieve targeted RNA degradation, akin to the mechanism of protein degraders, it would provide a new strategy for drug development.
A New Nucleic Acid-Based Strategy for TPD
In May 2018, Matthew D. Disney’s team at the Scripps Research Institute developed an RNA degradation strategy called Ribonuclease Targeting Chimeras (RIBOTACs). RIBOTACs are a class of heterobifunctional small molecules that achieve RNA degradation by specifically binding to target RNA structures and recruiting endogenous ribonucleases (such as RNase L) to these RNA molecules (Figure 1). This technology provides a novel approach to targeting RNA, particularly for RNA structures that are difficult to target with traditional small-molecule drugs.
In recent years, with advancements in RIBOTACs technology, RIBOTACs have demonstrated significant therapeutic potential across multiple disease areas, offering new possibilities for treating RNA-related diseases that are challenging to target with conventional small-molecule drugs.
Protein degradation technology at BOC Sciences
- RIBOTACs (Ribonuclease Targeting Chimeras) technology platform
- Targeted Protein Degradation Platform (PROTACs)
RIBOTACs in Antitumor Therapy
In August 2021, Matthew D. Disney’s research team developed a small-molecule RIBOTAC for RNA-targeted degradation by combining the tyrosine kinase RTK inhibitor dovitinib with a specific RNA structure (pre-miR-21). The RIBOTAC recruits the intracellular ribonuclease RNase L to specifically degrade pre-miR-21. Studies show that the RIBOTAC targeting pre-miR-21 (the precursor of microRNA-21) exhibits high selectivity and degradation efficiency for pre-miR-21 in both cell and mouse models. This significantly reduces miR-21 levels and alleviates disease progression in mouse models of triple-negative breast cancer and Alport syndrome (hereditary nephritis).
This research offers a new strategy for treating diseases such as triple-negative breast cancer and Alport syndrome, while also demonstrating the great potential of RIBOTAC technology in the field of antitumor therapy.
In May 2024, Professor Zhu Zhi and Professor Yang Chaoyong’s research team at Xiamen University developed an Aptamer-RIBOTAC (ARIBOTAC) strategy. This strategy combines the nucleic acid aptamer AS1411 with a ribonuclease-targeting chimera to specifically recognize and enter tumor cells, activating endogenous RNase L to selectively cleave specific miRNAs, thereby enabling precise cancer treatment. This chimera demonstrates outstanding capabilities in specifically recognizing and entering cancer cells, triggering localized activation of endogenous RNase L, and selectively cleaving miRNAs complementary to ASO.
By degrading oncogenic miR-210-3p and miR-155-5p, the ARIBOTAC strategy’s effectiveness and versatility were validated both in vitro and in vivo. These findings highlight the potential of the ARIBOTAC strategy as a cancer treatment approach by precisely targeting cancer-related miRNAs.
In June of the same year, Professor Jiang Jianhui and Professor Chu Xia’s research team at Hunan University introduced a novel inducible ribonuclease-targeting chimera (iRIBOTAC) strategy. This strategy achieves on-demand degradation of G-quadruplex (G4) RNA in response to bioorthogonal or cell-specific triggering factors, enabling precise cancer treatment.
RIBOTACs in Neurodegenerative Diseases
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive neurodegenerative diseases. The most common genetic cause is the hexanucleotide repeat expansion (HRE; G4C2 exp) in intron 1 of the chromosome 9 open reading frame 72 (C9orf72). This expanded RNA transcript, r(G4C2)exp, is toxic and plays a role in the pathogenesis of C9ALS/FTD. In October 2021, significant progress was made in the application of RIBOTACs technology for treating neurodegenerative diseases, particularly in ALS and FTD. Professor Matthew D. Disney and his team designed a RIBOTAC molecule capable of degrading pathogenic RNA in ALS and FTD, successfully inducing degradation of disease-associated mRNA in patient-derived spinal motor neurons and ALS mouse models, reducing related pathology.
Currently, research on RIBOTACs technology for Parkinson’s disease (PD) treatment is primarily focused on reducing levels of α-synuclein, a protein associated with the disease. α-synuclein is an intrinsically disordered protein, typically difficult to target with drugs due to the lack of small molecules capable of binding to its pockets. However, in January 2024, the team made progress in PD research by using RiboTAC technology to selectively degrade the corresponding mRNA, thereby reducing α-synuclein levels. The small molecule (Synucleozid-2.0) that targets the SNCA mRNA encoding α-synuclein and inhibits its protein translation was converted into a RIBOTAC—Syn-RIBOTAC. Syn-RIBOTAC can selectively degrade SNCA mRNA, significantly reducing the expression of α-synuclein and restoring about 50% of genes that were dysregulated due to the abnormal accumulation of α-synuclein. This marks another breakthrough for RIBOTACs technology in the field of neurodegenerative diseases.
RIBOTACs in Antiviral Therapy
SARS-CoV-2, an RNA virus, relies on its RNA replication process for viral proliferation. Degrading viral RNA can effectively inhibit viral replication and reduce viral production and transmission. In April 2024, Professor Zhou Xiang and Professor Tian Tien’s research team at Wuhan University developed a strategy based on ribonuclease-targeting chimeras (RIBOTACs) to degrade viral RNA for the urgent treatment of SARS-CoV-2. The researchers modified RNase L ligands at the sugar ring or base portion of nucleosides, which were then incorporated into the viral RNA. The modified nucleosides recruit RNase L to degrade the viral RNA, thereby inhibiting viral replication.
Studies show that the RIBOTAC-based strategy to degrade viral RNA has a significant inhibitory effect on SARS-CoV-2 at the cellular level. In hamster models, the approach inhibited SARS-CoV-2 replication and activity in vivo. This research provides a valuable new strategy for antiviral drug development and further expands the application of RIBOTACs technology.
Conclusion
Although RIBOTACs technology demonstrates immense therapeutic potential, it also faces several challenges in its development. These include the difficulty of developing high-affinity and selective RNA small-molecule ligands, as well as issues related to cellular uptake and bioavailability due to the relatively large molecular size. Nevertheless, scientists remain optimistic about its prospects, believing that with advancements in biological and computational methods, the discovery of more high-affinity and high-selectivity RNA and RNase L small-molecule ligands will further propel the application and clinical translation of RIBOTACs.
References
- Costales MG, Matsumoto Y, Velagapudi SP, Disney MD. Small Molecule Targeted Recruitment of a Nuclease to RNA. J Am Chem Soc. 2018;140(22):6741-6744. doi:10.1021/jacs.8b01233.
- Dey SK, Jaffrey SR. RIBOTACs: Small Molecules Target RNA for Degradation. Cell Chem Biol. 2019;26(8):1047-1049. doi:10.1016/j.chembiol.2019.07.015.
- Zhang P, Liu X, Abegg D, et al. Reprogramming of Protein-Targeted Small-Molecule Medicines to RNA by Ribonuclease Recruitment. J Am Chem Soc. 2021;143(33):13044-13055. doi:10.1021/jacs.1c02248.
- Fang Y, Wu Q, Wang F, et al. Aptamer-RIBOTAC Strategy Enabling Tumor-Specific Targeted Degradation of MicroRNA for Precise Cancer Therapy. Small Methods. Published online May 25, 2024. doi:10.1002/smtd.202400349.
- Min Y, Xiong W, Shen W, et al. Developing nucleoside tailoring strategies against SARS-CoV-2 via ribonuclease targeting chimera. Sci Adv. 2024;10(15):eadl4393. doi:10.1126/sciadv.adl4393.