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AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

arxiv.org

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Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#31

Post by bayesian_horse »

bawolff wrote: post #10

For people who know about this area: How far away is something like this from an actual treatment? I assume its pretty far, but is it the sort of thing where you basically have to test to see if it works and is safe-ish? Or are a lot more steps involved? What does promising in this context mean? Like is it the sort of thing that has a 50% chance of eventually being useful, or is it more like 1% chance? Regardless exc…

I'd say this paper forms the basis for pre-clinical trials. First in-vitro with cell cultures, then in model organisms...

So maybe a few years until first Human trials if they are fast? Maybe up to a decade for full approval? As to the chance nobody can say. Too many factors go into that.

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#32

Post by bayesian_horse »

RandomLensman wrote: post #9

This could be an interesting addition to other large scale drug discovery methods. Not totally sure how orthogonal it is to other methods and about the price point when use at scale - but nevertheless. I suppose the critical issue will be still that going from molecule to treatment, the success rate is annoyingly low. (And, yes, there are lots of attempts to increase the odds here.)

My impression was that arge scale drug discovery methods have largely failed....

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#33

Post by bayesian_horse »

didntreadarticl wrote: post #30

It would be great it we could find a way to use Alphafold to kindof reverse engineer proteins - like to specify the shape you want and then run Alphafold 'backwards' so that you're going from shape -> DNA instead of DNA -> shape

They mention a framework for protein design. But I guess you'd start out with a know sequence/structure and mutate it towards what you want.

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#34

Post by Closi »

ramraj07 wrote: post #23
fnands wrote: post #20

Earlier quoted context omitted.

Eh, I would argue there is a massive difference between drug discovery and patient care, which was what Watson was aiming for. Filtering out useful molecules from useless (or dangerous) ones is a nicely contained (if difficult) problem that ML is pretty good at solving.

To say Watson was aiming for anything is an injustice to the word Aim.

How about "Watson was aiming to sell consulting services"?

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#35

Post by _Wintermute »

bayesian_horse wrote: post #32
RandomLensman wrote: post #9

This could be an interesting addition to other large scale drug discovery methods. Not totally sure how orthogonal it is to other methods and about the price point when use at scale - but nevertheless. I suppose the critical issue will be still that going from molecule to treatment, the success rate is annoyingly low. (And, yes, there are lots of attempts to increase the odds here.)

My impression was that arge scale drug discovery methods have largely failed....

Apart from all the new drugs discovered over the past 30 years...

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#36

Post by xbmcuser »

mikkelam wrote: post #16

Offtopic: More and more I'm noticing the ever-increasing amount of chinese names in machine learning papers. Can anyone explain that? Are these researchers mainly choosing this field out of their own interest, or is China somehow pushing/sponsoring a lot researchers to pursue this field? I realise that China is pursusing AI dominance, is that just what we're seeing? Note this is purely curiosity, I have no problems w…

China population is twice the that of Europe + US. With the % of people going into science fields in China being a lot higher they are probably producing 4-5 person for a 1 person in EUR and US . This is not just in ML or AI but many other fields

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#37

Post by Gehtio »

jimmySixDOF wrote: post #14

Interesting to consider this in light of yesterday's news about the lack of success for IBM Watson in Healthcare. https://news.ycombinator.com/item?id=30046432 IBM’s Watson Health is sold off in parts

For me, what alphafold showed is probably one of the best and brightest teams technology wise and with Google the financial and resource availability.

When I think about IBM I think about a business company.

Google already added alpha fold into its gcp ai vertex service.

They make stuff very very end user-friendly and have been doing this with ai for a while.

The IBM health news was very disappointing to me and I would love to have more insight on it.

Until I have I will just believe that IBM is just not tech savvy enough or was to early technology wise.

Gcp also provides audit save and Industrie standards and complaince standards.

They go so far that they have contracts with pentagon and co. They also have the cooperation with the (or one of the biggest) healthcare providers in the USA tx to there complaince support on gcp.

After all GCP provides encryption on rest, in memory, with Google provided keys and customer provided keys.

They also have gvisor.

With the push of big companies like sap into the cloud, gcp aligns already to business companies globally.

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#38

Post by MeteorMarc »

londons_explore wrote: post #25

This paper looks more written for investors than as a scientific process for others to work from...

Yes, I do not know how to feel about this. On the one hand it is great that they found this and made the results public before trying any followup microbiological research. On the other hand, they seem to say: we, engineers, did in two years what you, scientist, failed in doing the last 20 years. They could have just written a clean scientific paper and mention AlphaFold in their methodology section.

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#39

Post by RandomLensman »

bayesian_horse wrote: post #32
RandomLensman wrote: post #9

This could be an interesting addition to other large scale drug discovery methods. Not totally sure how orthogonal it is to other methods and about the price point when use at scale - but nevertheless. I suppose the critical issue will be still that going from molecule to treatment, the success rate is annoyingly low. (And, yes, there are lots of attempts to increase the odds here.)

My impression was that arge scale drug discovery methods have largely failed....

Success rate is really low from an end-to-end perspective, but I would not call this a failure (and I expect the same from this approach). It reflects the difficulty of the task.

Re: AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor

#40

Post by fnands »

bayesian_horse wrote: post #28
rguiscard wrote: post #11

Several authors are in Insilico Medicine[1], which uses AI for drug discovery and has one product in clinical trials if I remember correctly. [1] https://insilico.com/

This paper doesn't use Machine Learning at all, as far as I understand it.

It does. They used Chemistry42 which is Insilico's ML based molecule generation platform(?)[0]. Sure, they didn't train any models specifically for this case, but they used a protein structure predicted by one ML algorithm, then used another set of ML algorithms to find and rank molecules that might match the protein, and then tested the most likely ones in reality.

[0] https://arxiv.org/pdf/2101.09050.pdf

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