Programmable icosahedral shell system for virus trapping | Hacker News Reader

Programmable icosahedral shell system for virus trapping

cacm.acm.org

88 pointsNextGenLog29 comments

> "Using computational genetic engineering, researchers at the Technical University of Munich (TUM) say they have invented a method of killing any type of virus. The researchers say they have demonstrated their solution on previously incurable hepatitis-B viruses, and are next aiming at the coronavirus.

The deoxyribonucleic acid (DNA) origami base-pair key-in-lock method they devised yields sphere-like icosahedral shells that kill viruses by clamping around each virion (the complete, infective form of a virus outside a host cell) until it is dead, dead, dead."

This sounds pretty amazing. Human trials being "years away" is no surprise, but here's hoping it gets there soon.

Sounds "simple" enough for an organism to evolve a defense system like this. Why it isn't present in current living forms after millions of years of evolution? Or if it ever existed, maybe it devolved.

Original paper: https://www.fradenlab.com/app/download/9774776565/s41563-021...

Edit: sorry for the previously bad link. Didn't notice.

From what I get, it looks like the traps basically smother the viral shell and prevent it from interacting with any surfaces.

They tried a couple methods to achieve this. Either assembling the shells around the virus, or starting with pre-assembled shells with a hole in them (an icosahedron with a pentagon missing.) For the latter case, they were able to neutralize more than one viral particle by making the shells big enough.

My main question is how the viruses find their way reliably into these preassembled traps.

> My main question is how the viruses find their way reliably into these preassembled traps.

I've always wondered that about enzymes, just one of the many reasons I'm not a biochemist.

Brownian motion means molecules inside your body move at ~10000kph (and because it’s random they don’t go anywhere). They’re bouncing around at that speed inside a 30 cubic micrometer ball.

At that speed they meet every other molecule. Not just meet, but touch them everywhere, at every angle, in every configuration.

> Subsequent in vivo (within a living organism) testing on mice showed the DNA-origami traps were capable of targeting individual virions inside the body, disarming them without disrupting bodily functions, and finally destroying them with natural immunological mechanisms.

It's wonderfully surprising that body can have bunch of free floating DNA constructs inside without triggering strong immune response.

> Subsequent in vivo testing on mice showed the DNA-origami traps were capable of targeting individual virions

... in mice.

Sorry, that's an in-joke:

https://twitter.com/justsaysinmice

https://jamesheathers.medium.com/in-mice-explained-77b61b598...

Mouse bodies, anyway.

> It's wonderfully surprising that body can have bunch of free floating DNA constructs inside without triggering strong immune response.

I would be very scared of a free floating DNA machinery therapeutic, as Lupus is associated with anti-dsDNA, (to be fair we don't know what direction the causal arrow is), and it's such a long and chronic condition that I would doubt the ability to model it in early stage preclinical or even find it in phase I safety. For some conditions phase 4 is way too late.

yeah this feels like a prime candidate for sci fi "good thing turned out to be a bad thing"

What happens to the millions of traps floating inside a person's bloodstream after they do their job? Do they eventually get dismantled by the immune system?

Maybe? It's formulated really badly, you don't know if they mean the virus or the traps...

"Subsequent in vivo (within a living organism) testing on mice showed the DNA-origami traps were capable of targeting individual virions inside the body, disarming them without disrupting bodily functions, and finally destroying them with natural immunological mechanisms."

DNA and RNA get degraded all the time..

free floating DNA is a pathogenic state of affairs and will be phagocytosed, the aptamer/virion complex will be shredded and the molecular debris is incorporated into antigen presenting complex initiating development of immunity

I would assume that with the rate the human body replaces blood they'd end up getting removed over time.

The traps require antibodies specific to the virus, so what's the advantage of this over other antibody therapies? Producing antibodies for therapies is expensive enough and producing DNA origami may not necessarily scale.

DNA apatmers are used all the time in science. The key will be productizing them for in vivo delivery. They would have to be immuno-reactive only when they bind their target and the response will need to be to the target and not the aptamer.

That’s APTAMERS btw for anyone reading

its good that you underscore that, there is the ADaptOmer that is also a DNA strand but is used as an adapter to bind two other molecular entities into an ADAPTOMER complex.

APtamers bind a single entity

This sounds like an even bigger story than the Moderna HIV vaccine trial post yesterday.

Don't think so. One is a promising-sounding experiment, the other is a serious effort by a company with a track record of delivering effective vaccine doses by the billion that already has something ready for human trials.

I guess this wouldn't work as a cure for HIV if it only kills actively replicating virus. Still amazing if it works in practice.

This is very cool. But the article doesn't say anywhere if the effect is high enough to cure disease.

Thought this was going to be about computer viruses and was wondering how traps could possibly combat it. But alas it's about biological viruses.

We already know that viruses play a role in cross species genetic transfer.

And we still don't 100% know if HERV serves some real purpose or not.

I hope this "all viruses" is "when we choose to go after specific ones".

Um, you go ahead and volunteer for cross-species genetic transfer experiments. I'll take the innoculation thanks.

Yep, it sounds like a (semi?)unique structure is required for each target virus.

> A specific combination of nucleotides is first modeled in simulation to be the correct size to handle the target virus

From the article:

> Dietz said the interior of the shells were coated with "antibodies specific for the hepatitis-B virus. You can think of the shells as a generic platform; depending on your selection of inner coatings, you can 'program' them to be specific for a user-defined target virus."

for my understanding its the combination of shell size and coating which does the targeting.

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