Genetic medicine is completely transforming the way we think about disease. Thanks to whole genome sequencing, we no longer have to group diseases purely by symptoms. We can identify the specific gene that might be responsible, which changes everything in terms of diagnosis, and begin to think about therapies that target the culprit gene directly.
This is where oligonucleotides come in. Oligonucleotides are designed based on specific genetic sequences and offer an incredible level of precision. A short strand of nucleotides can bind uniquely to a single target RNA allowing an incredible level of precision.
This precision is also one of the key strengths of antibodies or ‘biologics’. They offer a level of precision that small molecule drug development has lacked, but antibodies can only access what’s on the cell surface or circulating in the bloodstream. Oligonucleotides, however, can get inside the cell and shut down a toxic protein at its source.
In the early days of oligonucleotides, development focused on monogenic rare diseases, where the genetic cause was well understood and where lengthy target validation wasn’t necessary. For example, in Huntington’s disease, the causal mutation is an expanded repeat in a known gene, so the idea of using an oligonucleotide to ‘silence’ the faulty gene for patient benefit was no big step to take.
Nowadays we are more courageous and are thinking outside monogenic disease and small patient populations to larger, more impactful targets. In many diseases, we already know what needs to be targeted but have failed using other modalities. Some of these traditional drug targets, such as phosphatases or ATPases, have been incredibly difficult to address because the binding sites are often shared with many other proteins. This makes it nearly impossible to get the required specificity (and therefore safety) from a traditional small molecule drug.
Although there are some limitations, oligonucleotides ultimately help solve two huge problems in drug development: reaching the target and hitting it with accuracy. They provide exquisite specificity and are not constrained by the location of the protein.
When it comes to safety profile, oligonucleotides behave much like a class of drugs, so we’ve learned where the general red flags are. Yes, there have been mistakes and initially the regulatory pathway wasn’t set up for oligonucleotide drugs, which has slowed progress, but the industry is figuring it out. Unlike small molecules, where every new chemical entity comes with unknown toxicity risks, oligonucleotides are more predictable. With small molecules, you often don’t discover safety issues until it’s far too late – sometimes not until the patient stage. But with oligos, we know what to look for and how to test for it early on.
This also makes oligonucleotides relatively straightforward to design. The challenge lies more in the biology: understanding your target and what happens when you modulate it. Take Huntington’s as our example again. It turns out that we can very successfully remove the toxic mutant protein with our oligonucleotide approach, but the benefit hasn’t been the revolution we hoped for in patients and this is because a functional, normal version of the protein is still missing and is apparently essential. Toxicity in patients isn’t just about removing the mutant form – it’s also about losing the good version. That’s biology for you, and we face these issues with any modality.
Today, we have an even greater understanding of the potential benefits of oligonucleotides. They allow us to shut off the production of a toxic protein before it’s even made, or reshape it via altering RNA splicing into something that’s no longer toxic. These mechanisms of action are fundamentally different from traditional therapies and open the door to a new world of therapeutic options.
Boom, bust and formulation challenges
Right from the early days of oligonucleotides, everyone could see the potential. There was a huge wave of enthusiasm. Biotech companies sprang up, but many collapsed just as quickly. Big pharma also got involved, Millions were invested and lost.
Early on, one major issue was the cost of goods. Oligonucleotides are made synthetically, and the manufacturing process is more complex than that of small molecules. Over time, however, processes across industry have been standardized. Costs remain high but are slowly coming down as more oligo drugs reach the market.
Today, there is a huge focus on delivery. Oligonucleotides are not orally bioavailable and have no gastrointestinal absorption. This is a big shift for pharma, which is so used to the classic Lipinski Rule of Five and designing drugs that fit neatly into a target product profile. Patients want pills. Pharma wants pills. But oligos don’t play by those rules!
There are also delivery and stability issues. A naked, unmodified oligonucleotide, if injected, typically has a half-life of less than six minutes. Our bodies have evolved defense mechanisms specifically to eliminate foreign RNA (think viruses!) – which is a good thing for biology, but a challenge for therapeutic delivery.
Over time, the industry has developed chemical modifications that protect oligos from nucleases and enhance protein binding. Now, even though systemic circulation is still not fantastic (less than 24 hours), it’s good enough to push an oligo into tissue. Once in the tissue, it stays there – so the drug will remain active long after a single dose. The result for the patient is that although it is still an injection, it is very stable, which significantly reduces the burden of injection to once every few months.
Some groups are trying to develop oral oligos. Maybe one day we’ll get there, but the industry isn’t close. That said, the incredible uptake of GLP-1 analogs for weight loss shows that patients are open to injectables – even when the disease being treated isn’t life-threatening. That shift in patient behavior is a big deal – and oligos could benefit.
Another challenge is the restricted biodistribution pattern. Double stranded oligos, such as siRNA, do not cross the cell membrane by themselves and need either a lipid or a conjugate that will be actively transported into the cell. Single stranded antisense oligonucleotides (ASOs) will cross the cell membrane without delivery aids, but the large part of the drug will accumulate in the liver and kidneys. Diseases in these organs are good targets for oligonucleotides. Oligos are also successful in settings that allow for local administration, such as the eye. The skin is another area of interest.
But how do we deliver oligos to treat indications such as cancer? That’s still an ongoing challenge, but we have learned that conjugating oligos to other molecules, such as antibodies, peptides, and carbohydrates, can dramatically change where they go in the body. GalNAc conjugation, for example, has opened new doors. It has been clinically validated and shown 30- to 50-fold increases in liver uptake. The transferrin receptor is also showing similar promise for heart, muscle, and even the brain.
We're not yet at the point where we can pull a delivery solution off the shelf and plug it into any oligo, but we know how to approach it. Through collaboration between industry, academia, and regulatory bodies, we’ll get there.
Next-generation oligos
Today, marketed oligo drugs are generally evenly split between ASOs and siRNAs, but within the ASO category – especially the single-stranded DNA oligos – about half don’t work by degrading their target RNA. In other words, they don’t cause “knockdown,” which refers to reducing gene expression by destroying the messenger RNA so that the protein isn’t produced. Instead of degrading RNA, they act by steric hindrance, which means they can physically block certain interactions. The target might be an RNA-binding protein, or perhaps it interferes with the secondary structure and the structural stability of the RNA itself.
There are many things you can do with these steric blockers. What makes them unique is that they’re fully modified, which means they don’t recruit RNase H or the RNA-induced silencing complex to degrade the target. Instead, they sit on the RNA and block whatever was supposed to happen next.
So far, the most prominent application of this has been splice switching. Consider a patient with a mutation that confuses the cell’s machinery when it's trying to splice introns and exons. By masking that mutation, we can help the cell “skip over” the faulty signal – allowing it to correctly recognize and splice the necessary exons. It’s not 100 percent perfect, but there is clinical proof of concept that this approach can improve disease states.
We can also flip this approach on its head. Sometimes, we want to induce a splicing error. If we know that a particular exon contains an expanded repeat that will produce a toxic protein, we might deliberately exclude that exon. The result is a shorter protein that’s less toxic but still functional. Thus, oligonucleotides can be used to tell the cell: “Make a mistake – but make this specific mistake.” In doing so, the disease burden can be reduced.
The industry is also starting to look at RNA editing. If there is a mutation, you can trick the cell into correcting the RNA transcript after it’s been made, without changing the underlying DNA. It’s not gene therapy in the classic sense because it doesn’t permanently edit the genome, but the effect is still therapeutic – and can be sustained with repeated dosing.
Of course, delivery remains a challenge. These newer constructs are often larger, so getting them into the cell is more difficult. But the good news is that all the knowledge we’ve accumulated through aptamers, siRNAs, and earlier oligos applies. New generation oligos will benefit from the foundational work. It’s a rising tide that lifts all boats.
In science, new mechanisms are often discovered entirely by accident. We’re still just beginning to understand the full potential of oligonucleotides. We’re only seeing the tip of the iceberg. The basics are in place – we know how to make oligos, we know how to manufacture them and check for safety, and we know, broadly, where they go in the body. This has allowed the industry to focus on the low-hanging fruit.
It didn’t take much to ignite the field again. Just a few molecules for rare diseases, and then a big shift with Leqvio, which was the first time a major patient population received an oligonucleotide-based therapy. It was proof that the approach worked – and it brought investment back. Now the mindset is: “Let’s start again. Let’s revisit what we know about these molecules – and figure out how to maximize their potential.”
Don’t forget safety
It’s incredibly exciting to think about what we could achieve. For me, I still haven’t gotten over the first wave of excitement – the fact that you can inject an oligonucleotide and show consistent function in known tissues is an incredible advance. We know oligos get to the liver. We know they get to the kidneys. And they can also be used in the central nervous system. There are already so many disease indications that could benefit from what we have today, and I look forward to seeing what happens when we put these molecules to work on the right targets to solve human disease states.
I’m delighted to be able to make a small contribution to this exciting field. I see a lot of early-stage programs – many are very promising, with great data and potency. But although they may have nailed efficacy and proof of concept, safety for chronic human use is often neglected at the early stages. This is where my colleagues and I step in. We look at the program and ask: “What data do you have and what is missing? What do we not know? What are the red flags from a safety standpoint?” Then, we map out what needs to be done.
Safety is still too often overlooked. You need to take the right steps early on. Benchmark against known clinical failures. Use assays that are appropriate for oligonucleotide modalities. Look for the red flags – which should now be well understood across the industry. Don’t wait until you are in the clinic to ask, “should we check for off-target effects?” Do it early. Build it into your program from day one, the power of big data ‘omics is at your fingertips – harness it!
There are over 20 oligonucleotide drugs on the market and hundreds more in clinical trials. We’ve learned a lot. And the best part? The most potent and safest versions of these molecules – the latest generation of chemistries – are still in development. We’re already seeing great results. And there’s more to come.
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