They we want to
Stop these cancer cells
You know reproducing themselves. Mm-hmm. So we have a disease. So we have a purpose
That's great. And we have a target right? So there are a couple ways we can do this usually people do it all together
So you should start definitely literature know right know what's out there normal are doing
And you can take those molecules already into account for your search for your next step
Meaning others have tried to inhibit specific enzymes or okay, so you can do that
you also have a lot of enzymes have a certain percentage of
Similarity so you can you can look into similar enzymes that have been, you know widely studied
You know, like polymerase is for cancer. You have so many right and they always have a you know certain percentage of
identity
so that's one the second one we can let's say that you know, we know someone that
started a company and
They actually were going for another treatments and they actually saw that day or enzyme
You know actually targets one of these polymer races. So that's another one right? We just use
These unexpected results from other companies that are actually you know
Not gonna work on it
You have this molecule that you wanted to do something and then you find out does this other thing?
Well, then you just run with that and see what you can do with that
Right or you see why you know, why is this molecule actually doing this why we thought was actually gonna do something completely opposite
Then you know the other option which is very used nowadays is the high-throughput screening, right?
so we have a chemical library and we just screen thousands and thousands of compounds for the target that we are looking for and
so then we get
hits and
We choose, you know, our thresholds and our values and then we analyze those molecules
So let's say that we start with that actually before we go. Let me I want to really understand
so there there are we talking like in vitro like a bioassay is that I don't know or-or-or we can also do like
simulations - right right
So, uh, all of that comes kind of together
I would say but let's say we start with the screening and then from those
Their library of like 10,000 or 20,000 compounds you can have anything from like ten thousand to a hundred thousand
These are small molecules a couple couple dozen atoms or so. Yeah small molecules
And you know, these bioassay is actually looking to our target the one we want. So let's say out of that we get like 250
results, right so
you know here also varies a lot if you work in academia if you work in industry or you know
If you and I are starting a company or our cancer research
How much money we have so, you know, it's gonna vary a lot of things but let's say from those 250
Compounds we are gonna analyze them some of them manually. We are gonna see what do they have in common?
We might be able to use some software's that actually, you know do this for you
but let's say you know in the lab you do a manually you look at them you see
What they have in common, right and then you start cutting or you start seeing okay?
These part of the molecules is same for everything. So let's just go with that, right?
So we're able to from 250, you know get it down
and then
from there
You start the computational analysis, right? So, okay. So it's it's it's you in the lab first
What varies this is usually a cycle? Right? So you get you have some molecules in mind that you find through, you know?
Whatever path you found them and what are you physically doing?
You're you're you you need some biological material, right? You need some cells
For the
how does the bioassay work I don't even know is what I'm sayin so that kind of comes later, but
The high-throughput screening is a very robotic
You know I say they do have their own assay
of course and usually just comes with some sensors right like fluorescence and things that give you oh
You're just looking for properties of the molecule. You just look for like binding affinities for the molecule to that
That okay that time so we're just looking at how this interacts with the enzyme. That's right
so, you know, usually let's say the less color you get the fluorescence you get and
Biggest affinity or it does vary on the asset though. Mmm less floor. Okay, so the okay. Yeah
Everyone has a difference right? It has some property but then when it binds it does less of it we can see you can
Write and so then all of these you say, okay
There's 250 and then like these ten were the best and they all have a carboxyl group right here or something
So that's a really important feature. Yes
So then you see that one has a rink or there one who's like a three ring? So you kind of
Analyze them and combine them into you know types of molecules. Let's say okay, right?
So let's say we gave we have one with three rings. That is aromatic the other one. He's just a linear molecule
And then the other one, you know
Whatever we can come up with right that we see so
Then here is when you start you can either go to the web and start synthesizing and here is when the cycle starts so
Let's say we there is one day we really think that's it. Right. So we're gonna go to the lab
We're gonna make these molecules right? It's like a puzzle. Yeah, and we're gonna talk a lot about that, right?
So we're going to put pieces together and we are gonna get these
Molecules so the potion-making and some friends. They're used to you know, call me a potion makers. Okay?
so you you have that and then
If you do these bio assays and that's you know, very that's you have to collaborate with biology
so if i'm a chemist by training
I'm usually not doing these assays but we have colliders right and and so those asses they come, you know with pharmacokinetics pharmacodynamics
You know all those properties that we need to look at. Mm-hmm. So you look at that and you see
Okay, this is good values, but it could be better
Okay, better binding better binding better potency
You know better outcome pretty much between the target and the molecule
So once we have those numbers, all we have to do is something called structure activity relationship
Which means you keep improving and changing your molecule
so that you try to optimize your outcome remove a carbon over here turn this carbon into an oxygen this
Slightly toy with the is that where the computer comes into play?
So yes
the computer helps here a lot because once you are able to actually get like a
crystallography structure of your molecule with the protein or you know the enzyme
Then you look at it in the computer and you actually see pretty cool some reality right now. So
That's fascinating. So you've got the enzyme and you know, the you you know
The primary structure and you've got the active site and then you take your little molecule you plop it right in there
And then you see oh like this interaction is happening here this iner and then you you do you then?
Hypothesize as to how the inhibition is occurring like whether there's a covalent linkage like a serine like a tax
Right here, and then that and then that ruins the enzyme and that's kind of a thing. Ok
Yes, so you look at it and you see ok
So if this part of this mouse the molecule is completely inside the pocket then he means it's very important, right?
So we need to optimize this part of the molecule and just make these bonds stronger. Ok. So then if you look at those
amino acids in the protein around and you can see oh, you know if we add like
Carboxylic group here. Then we can have a hydrogen bonding with that amino acid and even stronger. Yeah
These are the interactions that are probably happening
so if we make these changes and we don't have impact the the the general shape of the molecule, but we just add a
Change to a particular atom that will make us stronger, right?
Interaction help and you can actually look alike distance, right?
so you see oh
I mean this group here just needs to be a little bit longer so that it actually sits in that perfect spot
Then you just go back to your molecule and do that insert a carbon just click a button and in the car