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The success of any research project depends on its ability to bring results to the marketplace.
RNA drugs: hitting the target
The theoretical appeal of RNA drugs is tempered somewhat by the multiple barriers that impede their development. Now, a large scale international collaboration based at the University of Copenhagen is paving the way towards safe and effective drugs fro the treatment of human disease..
The traditional approach to treating genetic and infectious diseases and disorders involves the targeting of relevant proteins. These proteins differ widely from one to the next, and the drugs (e.g. antibodies or small molecules) that target them are likewise unique; one cannot simply take the blueprint of one drug as the basis for another. Since the late 1970s, however, the potential of RNA drugs has provided a promising alternative that has kept scientists busy the world over.
Heading straight for the messenger RNA (mRNA) that encode proteins, RNA drug development benefits from the similarities that exist between these RNA molecules. The knowledge that enables the design of one RNA drug, therefore, is to some extent transferable. No longer does each therapeutic need to be entirely considered anew.
Despite the great strides that have been made, the potential of RNA drugs is yet to be fully realised as major challenges exist concerning off-target effects, tolerability and the potency of these therapeutics. Today, these issues are at the forefront of the work being carried out at the Center for Computational and Applied Transcriptomics (COAT). A newly established cross-disciplinary enterprise, COAT aims to facilitate the design of safe and effective RNA drugs through the integration of experimental biology data and cutting edge computational methods.
Led by Anders Krogh, a professor in bioinformatics and head of the University of Copenhagen’s Section for Computational and RNA Biology, COAT brings together the expertise of the Danish universities of Copenhagen and Aarhus, the University of California Santa Cruz (UCSC), New York’s Memorial Sloane Kettering Cancer Center (MSKCC) and the biopharmaceutical company Roche Innovation Center Copenhagen (RICC).
Enabled by a €5m grant from the Danish Strategic Research Council, the centre’s work marks a vital contribution toward the functional annotation of the human genome, an endeavour that promises to narrow the gap in our understanding and treatment of genetic diseases in humans.
The initial excitement surrounding RNA drugs stemmed from the simplicity of the concept. “It’s really easy in principle to design an RNA drug that targets mRNA,” states Krogh. “In a disease in which a gene is over-expressed, you can in theory synthesise an oligonucleotide (oligo) that turns this gene off. All that is required is an oligo that reverse complements a gene’s mRNA to enable binding. It’s easy on paper, but in reality it’s proven a lot harder to find oligos with all the right drug properties.”
The structured nature of mRNA is, quite literally, an obstacle to RNA drugs. Not only do oligos need to be complementary to the target mRNA, but they also need to target regions that are accessible. “mRNA fold into what we call a ‘secondary structure’, so it can fold into structures much like proteins can,” explains Krogh, “If they are structured then the oligo can’t bind to the target.” A further encumbrance to RNA access is if a protein binds the target site.
The advances in DNA sequencing that have occurred in the last ten years allow the team at COAT to investigate how these oligos target mRNA with a particular view to the accessibility of RNA drugs. The ability to perform transcriptome-wide sequencing and the like provide the tools for analysing the binding sites of the huge amounts of short RNA sequences involved. For instance, the centre was recently able to report significant improvements in the methods for probing RNA accessibility. Using a massive parallel-sequencing-based method called hydroxyl radical footprinting (HRF), COAT have arrived at a way to discern the structure of mRNAs to an unprecedented degree. “Although not completely accurate, our method for probing combined with computational methods for prediction gives us very good estimates of mRNA structure and hence accessibility to RNA drugs,” Krogh remarks.
Although drugs are designed with specific mRNA targets in mind, there can be a tendency to stray off target and include other genes in their effects. In essence, the drug will manage to suppress the gene it is meant to but then reduce the expression of other genes with coincidentally similar sequences. These ‘off-target’ effects can cause significant problems in the development of a drug. In order to study these effects, the team at COAT has been developing a method that can experimentally map all the binding sites of an oligo. Beginning with tens of thousands, the method reduces the number by selecting oligo sequences with the minimal amount of close sequence matches to unintended RNA targets.
One of the centre’s most exciting discoveries concerns the problem that many oligos are poorly tolerated. This was of very practical importance to COAT’s industrial member at Roche Innovation Center Copenhagen, where Morten Lindow has been struggling to find ways to identify and get rid of oligos with low tolerability. The fact that an oligo has low tolerability (essentially meaning it is poisonous) may not emerge until toxicity is evident in murine models, quite some way along the road of drug development. However, Lindow and his colleagues were surprised to find that from sequence alone it is possible to predict toxicity. “People were expecting that it would be more complex to discern and would involve all kinds of investigations” says Lindow, “but it was quite simple.” It’s not yet possible to make predictions that are a hundred percent accurate, but it has already radically reduced the amount of experiments that are usually necessary. If a drug is predicted to be very toxic, RICC doesn’t even begin to test it.
Established in 2011, the COAT has achieved a considerable amount of success in its short life. Naturally, Krogh expects the research carried out between the partners to continue in academia, but it’s hoped that COAT will be able to carry on the relationship that’s been built with RICC beyond the current 2016 timeline for the centre. As more is learnt about the structure of human RNA and protein-RNA interactions, it’s a relationship that could see the future of RNA drug development realise its potential at last.
Published: Wednesday, 3rd August 2016