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We Made One Gram Of Remdesivir

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Re: We Made One Gram Of Remdesivir

#101

Post by CamperBob2 »

rwmj wrote: post #86
Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

To what extent can synthesis steps be automated? Do you use a computer to plan how to get to a chemical? Do you use robots to carry out some or all steps?

I asked this question once. I couldn't figure out why there's no SPICE for chemistry (SPICE being any of several accurate, refined, and well-understood simulation programs for EE work).

You know the whole deal with the three-body problem? How closed-form solutions become intractable in a hurry once you go past two or three mutually-influential orbiting bodies? As it was explained to me, that's why there's no SPICE for chemistry. Modeling exactly what happens when complex orbitals with dozens or hundreds of electrons interact with each other is one of those things we just have no clue how to implement in a practical application.

Re: We Made One Gram Of Remdesivir

#102

Post by xg15 »

kccqzy wrote: post #22

Remdesivir is an analog of adenosine, one of the four building blocks of RNA. Just look at the main structure and you'll agree they look similar. It turns out the mechanism of action of this drug is that it's supposed to be confused with adenosine, so that the viral RNA replication process uses remdesivir instead of adenosine, which later breaks the RNA†. Our body, or really, all biological processes can synthesize i…

Out of curiosity: We seem to have a very good understanding how synthesis in biological processes works (from DNA to the eventual molecules), we are able to create DNA/RNA molecules with arbitrary content and we're increasingly able to simulate what molecule a particular nucleotide sequence would produce.

So, putting the three together, would it be possible to use actual biosynthesis for designed molecules by basically writing your own DNA/RNA and inserting it into a cell?

(Or is this already what's being done?)

Re: We Made One Gram Of Remdesivir

#103

Post by lazyjones »

Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?

Re: We Made One Gram Of Remdesivir

#104

Post by londons_explore »

lazyjones wrote: post #103
Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?

This is especially true since the number of possible "instructions" is pretty low. Heat it, cool it, mix it, filter it, centrifuge it, compress it, take a sample and put it through a test instrument.

Pretty much all chemistry is some sequence of the above.

Re: We Made One Gram Of Remdesivir

#105

Post by xg15 »

eyegor wrote: post #20

This article really reinforces my choice to drop ochem in college. It's funny how deciphering assembly code seems downright mundane compared to this jargon. Like, I get how given the process you could recreate things, or you could devise possible reactions based on electron shells and bonding tendencies, but how do researchers even figure out how to make these reactions happen? Especially when they require -100C, or…

Not a biologist or chemist, but the articles I've read that invoke biochemistry or molecular biology always reminded me of the intricate mechanical automata that were constructed before electricity could be used for computation.

Back then, you had a certain number of mechanical properties in mind as well as well-known "parts" (gears, linkages, etc) that you could predict the properties of very well - and the task was then to assemble them into larger mechanisms that did what you wanted them to do.

Seems to me, the intuition here could be similar - except the number of dimensions in which parts can interact is larger, the "clockworks" are orders of magnitude more complex - and your tools are much more coarse, so mostly, even if you know what you need to build, the building itself can only be done indirectly.

Re: We Made One Gram Of Remdesivir

#106

Post by LeifCarrotson »

lazyjones wrote: post #103
Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?

I'm a controls engineer. We're very good at making machines that will do a single process over and over. It's insanely difficult to do arbitrary processes with one machine.

Re: We Made One Gram Of Remdesivir

#107

Post by EL_Loco »

lazyjones wrote: post #103
Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?

There are machines that do this. Prety expensive though. Maybe too expensive for a uni's department where there won't be enough work to justify the machine's price?

Re: We Made One Gram Of Remdesivir

#108

Post by spockz »

fouc wrote: post #59
Vaslo wrote: post #34

In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…

Sharing failures seems like the best way to make progress. I mean we're talking about SCIENCE here. If we don't have a comprehensive list of what does not work, that's just going to make progress so much slower.

I also wonder how many breakthroughs we would not have because of somebody saying that something didn’t work.

Re: We Made One Gram Of Remdesivir

#109

Post by endorphone »

Chemistry is absolutely fascinating. One of my long-time goals has been to make a learning chemistry game of some sort. Players building bonds and molecules, solving problems by creating reactions, etc. Orbits and ions and quantum states.

Something truly educational, and of course one of the people I wanted to educate was myself by forcing myself to learn much more than my high-school level of chemistry.

I've gone down this road a few times, each time giving up on the absolutely scale of even the most rudimentary understanding.

Re: We Made One Gram Of Remdesivir

#110

Post by wuschel »

LeifCarrotson wrote: post #106
lazyjones wrote: post #103

Earlier quoted context omitted.

As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?

I'm a controls engineer. We're very good at making machines that will do a single process over and over. It's insanely difficult to do arbitrary processes with one machine.

Hi,

That is a very good question. In my PhD I built, among other things, a very primitive parallel stirring system in order to speed up the synthesis of test batches. Although a very crude device, there was tons of stuff that I needed to optimize.

There are many steps in the practical work that is chemical synthesis. It might be removing air, adding reagents in different elemental states, cooling/heating/keeping and certain temperature, observing the reaction, taking aliquots, terminating reaction, and the many steps of purification.

I'd argue that while automation is possible to a certain degree (continuous reactor systems are the most the most interesting IMHO), the resulting mashines are always problem (reagent, reaction, etc) specific. And here lies the problem.

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