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Researchers here have developed a system that directly targets and degrades viral RNA, which can be adapted to fight many viruses including that which causes COVID-19.

Scientists have rapidly developed vaccines against SARS-CoV-2, which causes Covid, but the rise of variants means the vaccines must be constantly modified. Ideally, therapies would target mutation-resistant viral proteins, but this has proven difficult.

But now researchers from Professor Gonçalo Bernardes’ lab have developed a system that directly targets and degrades the viral RNA genome. The new method can be adapted to fight off many viruses in addition to SARS-CoV-2, as well as treat various diseases. The research is published today in ACS Central Science.

Targeting RNA

Vaccines and antiviral drugs typically target proteins critical to viral infection and replication. This creates evolutionary pressure for the virus to mutate, which reduces the effectiveness of treatments and requires development of new vaccines and drugs. To get around this issue, researchers have turned to targeting highly conserved structures within the viral RNA genome.

Other groups have tried this approach. The best-known method is to link small molecule RNA binders to ribonuclease L ligands (RIBOTACs). However, this method has turned out to have its limitations because these types of RNA degraders rely on ribonuclease expression within cells, which vary across tissues.

To avoid this issue, first author Dr Sigitas Mikutis and Professor Bernardes envisaged a small molecule which could degrade RNA in a targeted manner by being in close proximity to its target. To accomplish this, they designed a compound with three components. “Where this research stands out is that we’re using small molecules that can degrade RNA without relying on other biomolecules, which is different from what other researchers are doing,” said Mikutis.

A three-part compound

For the first component, the researchers needed a small molecule which binds to RNA structural motifs found on the genome of SARS-CoV-2. They decided to try pyridostatin (PDS), which binds to G-quadruplex RNA structures, and also MTDB, which binds to betacoronaviral pseudoknots.

Second, they added a long flexible linker, which could reach multiple positions on the targeted RNA. And finally, they added an imidazole, the sidechain of an amino acid histidine, present on many ribonucleases. The new compound has been dubbed a “proximity-induced nucleic acid degrader” or PINAD.

Degrading the virus

In collaboration with Dr Konstantinos Tzelepis’ laboratory at Wellcome-MRC Cambridge Stem Cell Institute and researchers at Instituto de Medicina Molecular João Lobo Antunes in Lisbon, the researchers found that both PINADs degraded SARS-CoV-2 RNA when brought into proximity. In addition, the compounds were effective when tested in cells infected with SARS-CoV-2 and its alpha and delta variants.

Importantly, when the researchers gave the MTDB degrader to mice infected with SARS-CoV-2, viral load was reduced, as were levels of a biomarker of viral infection and replication.

Bernardes said: “This work provides evidence that it may be possible to weaponise RNA binders to destroy disease-related RNA structures”.

Targeting other diseases

The researchers say that their system should allow any RNA-binding small molecule to be converted to a PINAD, so that it could someday be used to target and destroy other disease-related RNAs. “We essentially showed that there are numerous structures that can be targeted, and that our approach can be useful for most of these structures,” said Mikutis. This list could include disorders such as Alzheimer’s disease or Huntington’s disease, targeting the mRNAs of misfolded proteins that have otherwise proven difficult to target.

The authors acknowledge funding from UK Research and Innovation (UKRI), the Wellcome Trust, the Jardine Foundation, the Cambridge Trust, the Agencia Estatal de Investigación, the UKRI Medical Research Council, Leukemia UK and Cancer Research UK.

S. Mikutis, M. Rebelo, E. Yankova, M. Gu, C. Tang, A. R. Coelho, M. Yang, M. E. Hazemi, M. Pires de Miranda, M. Eleftherious, M. Robertson, G. S. Vassiliou, D. J. Adams, J. P. Simas, F. Corzana, J. S. Schneekloth, Jr., K. Tzelepis, & G. J. L. Bernardes (2023). Proximity-Induced Nucleic Acid Degrader (PINAD) Approach to Targeted RNA Degradation Using Small Molecules, ACS Central Science.

From University of Cambridge