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A New Generation of Antisense Oligonucleotides (ASOs) is on the Horizon

March 30, 2023 by Dr. Stan Crooke

Thanks to advances in understanding the molecular mechanisms by which gapmer phosphorothioate (PS) ASOs result in the effects observed, a new generation of ASOs is nearing clinical testing.

ASO technology continues to advance rapidly. This is one of the differences between antisense technology and other validated, broadly enabling technologies. In this post, I will explain how this new generation of ASOs came about, how these novel ASOs differ from current classes of PS ASOs and why you should care.

First let’s talk about the most important attribute of a drug of any class: its therapeutic index (TI). If you have read earlier science posts or listened to the n-Lorem podcast series, you have already heard about this important attribute. In simple terms, the TI of any drug is the dose at which a meaningful adverse event or toxicity is observed divided by the dose needed to induce the desired effect. Because the most accurate part of a dose-response graph is the mid-point, pharmacologists prefer to compare the dose that results in 50% of the maximum toxicity to the dose that results in 50% of the maximum desired effect and these called the effective dose to produce a toxicity (ED 50, Tox.) and the effective dose to produce benefit (ED 50 Ben.) So, the equation looks like this:

Therapeutic Index (TI) = (ED 50 Tox.)/(ED 50 Ben.)

As a general rule, the higher the T.I., the better the drug.

Most advances in science are incremental, but occasionally advances are stochastic, that is the scientific field takes a giant step.

That is what happened in 2019 when Wen Shen and other colleagues and I published a paper in Nature Biotechnology (Shen et.al. Nature Biotech. (2019), 640-650) and it only took 30 years.

This seminal publication showed, for the first time why some ASOs were toxic and what led to the toxicities we observed for many years. Not only did we now know what caused these toxicities, we had a simple solution to avoiding them in the future. 

The observations we observed that had perplexed us for many years are as follows.  If we studied many members of an ASO chemical class like PS 2′-O-methoxyethyl (2′-MOE) ASOs, we could find many effective and safe ASOs, but some ASOs appeared to be toxic.  As we advanced to more potent ASOs, like PS 2’ constrained ethyl (cEt) or locked nucleic acid (LNA), we found many more toxic ASOs and the toxicities were worse.  These observations showed that the sequence of ASO and the 2’chemistry seemed to be related to the toxicity of ASOs. By knocking out RNAse H1, we were able to report that RNAse H1 was used by toxic ASOs to cause the toxicity. So naturally, we thought that the toxicities must be due to our ASO binding to RNAs in addition to our target RNA.  However, the more we studied these phenomena, the more the data didn’t fit this hypothesis. Then in the 2019 Nature Biotechnology paper, we proved that the toxicities had nothing do with RNA, but rather interactions with certain proteins and RNAse H1 that led to a toxic aggregate.  We showed each step in the process and that a very simple modification at one position in the ASO could virtually ablate the potential for toxicity while having little effect on the dose need to produce benefit, or said another way, a large increase in TI. We now have even better ASO modifications that can be used to eliminate the potential for toxicities while maintaining potency and lengthening the duration of beneficial effect. Those ASO designs are nearing clinical testing.

Now, why does that matter to you?

Well, this means that we can give higher doses of ASOs safely. This in turn means we may be able to produce even greater benefit in the tissues we are treating at n-Lorem. But there is even greater potential benefit to tell you about.  We know that our ASOs distribute widely in the body after subcutaneous injection, but at low doses, most of the ASO ends up in the liver, kidney and fat cells. If we raise the dose, we can then get ASOs in other tissues like muscle and the heart and show benefit in those tissues, but historically at the doses required to show benefit in muscle and heart, we observe too many toxicities.  Now, using our new safer class of ASOs, we could SAFLEY dose at higher doses and begin to treat patients with problems in the heart or muscle or other tissues. That is potentially a really big deal!

When will n-Lorem be able to take advantage of this new design?

Of course, we are very cautious because we do not want to add side effects the burden that our patients must live with. So, before we try these new ASOs at n-Lorem, we will want Ionis to get meaningful clinical experience proving that what we have seen in cells and animals hold true for humans. So, it will be a while before we incorporate this new ASO design at n-Lorem, but I am optimistic that the clinical experience will be positive. It will take a while, but I think it will happen. And when it does, it means that we can expand our reach to nano-rare patients with involvement in muscle and heart and potentially other organs. So stay tuned with us as we keep an eye out on the clinical experience of Ionis with these promising new ASO designs.

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