Now, last time we left off, we had taken you up through the stages of these nine stages.

We'd taken you up from the target identification stage, to hit ID, and now we're at the hit to lead stage.

And the key thing about this stage

is that we want to identify compounds that don't just bind to the protein,

they actually work inside a cell. And they actually show selectivity in a cell.

And this is yet another elevated level

and gets us closer to what we want, which is a drug that's safe and efficacious in people.

The key aspect of hit to lead stage is an iterative process in which we

not only show that the compound works in a biochemical assay,

but we also demonstrate that it works effectively and selectively in a cell-based assay.

So, it can actually go through the cell membrane, reach the target inside the cell,

if it is an intracellular target,

and engage that protein in a cell-based assay.

So, in starting this process, the compounds start off with potencies

that are weaker than we would like.

As shown in this biochemical binding assay

what we're looking for is compounds that will make the medicinal chemistry

that will improve the potency of the hit compound at least a factor of ten,

ideally a factor of twenty, in the biochemical assay.

We'll also be looking for things that start off with, from the hit stage,

that have weak cellular potency, shown here,

but with medicinal chemistry that correlates with the biochemical potency above,

drives the cellular potency to be more potent in the cell.

And this is all toward, the goal here is to get potent compounds

that are cell active.

Now, we also look in this stage for several other important properties.

For instance, we don't want it to bind to other off-targets

that are related to it that may cause toxicity.

So, what we'd prefer is that the compounds have potency that are at least ten-fold weaker

to the closest related target.

We'll also be looking to see that there's chemical evidence that we can advance these compounds.

When we look at compound's structures,

you should see that there are compounds which both

affect the target and compounds which don't affect the target

that are fairly closely related

suggesting that they're binding to a single site.

Because one of the properties of a drug is that it bind to a single site

on the target protein.

We'd like to know the molecular target; Michelle mentioned

that you can start off these hit-finding expeditions

just looking for cellular activity.

In that case, we don't really know the target that's involved.

At this stage, we really would like to have a molecular understanding of what that

small molecule is engaging.

Lastly, and very importantly,

in this especially for formulations reasons,

we look to have compounds which have solubilities above a hundred micromolar.

And that's because we wish the compounds to be

soluble and dissolve well once they're administered to an animal.

Ok, having successfully passed this stage,

of a hit to lead stage,

we're now into this very important and pivotal stage,

called lead optimization.

This is where we're looking to see that compounds that we've created

can actually work in a whole animal, can reach the

protein target, through a cell, and through the circulatory system of the animal.

Ok, so I think at this stage it would be good to understand

what happens when you swallow a pill.

Here's our patient right here, going to take a pill,

there's the pills, they go down through the saliva

into the stomach, where they're

subjected to pH one, so they have to survive that.

They come out of the stomach and they go straight into the duodenum,

which is this arrow here, which you see goes straight into the intestines.

Now, the intestinal, the intestines have about

two hundred square meters of surface area to absorb.

That's about the size of a tennis court.

There's a lot of opportunity to absorb a drug,

but it has to have the right physical properties to get across that intestinal barrier

so it actually enters into the blood stream.

Once it does get across that, into the intestine,

and into the bloodstream, the first thing that is does is

it goes straight into the liver through the portal vein, here,

and then meets a series of very important obstacles.

They include a variety of enzymes that are in the liver that are meant to detoxify,

get rid of, these foreign small molecules.

So, they would be things like p450s, which oxidize the compound,

or hydrolases, protease, lipases, esterases,

that would be hydrolyzing compounds.

There would be glucaronidation enzymes and the like,

which tag them so that they can be rapidly excreted.

Of course, all of these things can reduce the potency and the availability of the drug

to have its effect in the peripheral tissues where it's probably got to act.

So, if really does, the drug has to get through this very important gauntlet here,

of the liver in order to go on from there, throughout the circulatory system

first into the right atrium, then into the lungs,

and then back through the lungs, into the left atrium,

and then through the arterial system all the way throughout the body.

So, understanding the pathway that a pill has to take

is actually very important in this drug discovery process

because even though a compound could be great in a biochemical assay or a cell based assay

if it doesn't work in this system over here

then it's not going to be a drug.

Ok, once, now understanding that

and having successfully passed the hit-to-lead stage we're now ready to do lead optimization.

And that again is an iterative process of chemistry and biology

paired together. But this time, at the animal level.

So, the very first thing that happens when you have compounds from the hit-to-lead stage

is that you'd want to determine how well do they survive in the body.

How long do they live in the body?

And to do this, you typically give either an injection of the compound

or feed an animal this compound

and then determine the PK of the compound

in other words, how well does that compound,

this is time along the x-axis here and amount of compound

that's in an animal along the y-axis

and as the compound is injected, you see that there's a rise

in compound levels as it reaches, as it goes into the circulatory system

and then it decays.

And this half-life and other parameters

are used to judge how well will that compound work in an animal

or how long it will last in an animal.

The next stage is called the pharmacodynamics part of this

and there we're actually looking to see how active is this compound

in an animal model.

This, I show here, is an example of a xenograph model for cancer.

This, for instance, is time along the x-axis and along the y-axis is tumor volume.

You can see if the animal is untreated with your drug,

your drug candidate, the tumor grows rapidly,

that's this blue line here,

and then, in the case of a compound that shows some efficacy,

if treated with the animal, treating the animal with that, you can see you can suppress the growth of the tumor.

That would be a good result.

Now, one would continue along this process

of lead optimization until one has gotten compounds

that show good PK and good animal efficacy

according to those guidelines that we discussed at the beginning of this lecture.

The notion of lead optimization is really one of

trying to push compounds from the vast amount, trying to identify compounds

from the vast chemical space that's out there.

We, through the hit-to-lead process, we've identified potent compounds,

both biochemically and in cell assay,

we use pharmacokinetics to identify those compounds that have both potency and good pharmacokinetics

so we take compounds within this area of the Venn

and then using our animal efficacy experiments, our PD or pharmacodynamic models,

we're really interested the compounds that are sitting right in this narrow area here.

So, it's this iterative process of testing these compounds

in pharmacokinetics, pharmacodynamics and cell and biochemical assays

that ultimately then identifies a compound that can be deemed a clinical candidate.

This would be a compound that would be ready for IND enabling studies

and hopefully on the pathway to being a drug.

So, the goals for an oral drug, then, after this process

again are that we're looking for compounds that can be dosed

once a day, at hopefully less than a hundred milligrams per day,

we want reasonable protein binding potency

and reasonable cell activity.

We want a decent half-life, so that it only has to be taken once a day

and we want good oral uptake

so that it can be taken orally.

Ok, all of this work I told you about,

this reminds me of this Greek myth of this character down here,

who you can see is exhausted

and that's how you feel once you get to the clinical candidacy stage.

You've just spent a lot of time, a lot of effort,

from target ID, hit ID, hit to lead and lead optimization,

you've just reached this plateau here and now you look up

and there's all of this stuff still to go

because that's the drug development stage that you need to get to to finally reach the nirvana.

So, now having worked all, done all the work in the drug discovery part,

which is basically this area from target ID to, through lead optimization

to identify a clinical candidate,

that typically takes somewhere around three to four years to go through that process.

There's still a whole lot of work to go on.

From IND enabling all the way through registration and FDA approval.

This process is an even, much more expensive and longer process,

about four to eight years to get through that process.

And it's worth considering what are the,

what are some of the reasons that compounds, we should this as a funnel,

because there's a lot of attrition that goes on in this process.

In fact, when a compound enters the clinic,

here in phase one, only one in ten compounds will actually make it to being a pill.

What are some of the reasons that they don't make it all the way to being a pill?

About a third of the reasons are due to lack of efficacy.

So, this is, when a compound shown to be efficacious in animals

and all of the target ID experiments that were done before,

this really reflects the fact that we didn't have a validated target

to begin with. That there's more going on with the biology than we thought

and it's sort of back to the drawing board

about what is actually driving that.

Other reasons for compound failure

is about a third of them die because of toxicity in humans.

These are things that we couldn't really model in animals

and so they wind up being disqualified as, they may have failed in phase one.

Other reasons for failure are pharmacokinetics,

they just don't have the right clearance

and the right properties to be a once a day or twice a day medication.

And, so they can fail for those reasons.

There's another, and much less likely failure,

which is due to commercialization reasons,

and this may be because the company just feels that the market size is not what they thought,

the drug is really not going to be worth developing further.

And so they will stop that.

There are many other reasons that might happen,

but these represent the lion's share of the kind of failures that happen in the clinic.

So, we really need to get much better at doing this.

We know that healthcare costs are spiraling out of control

and this represents something like fifty to twenty percent of the GNP

and new drugs and new therapeutics can really

spare us a lot of money in our economy if we're able to find new compounds that can ameliorate a disease.

Because it's much better to treat it early than to have to deal with the symptoms

and the ramifications after.

This also highlights the fact that we need to get to

prevention and cure, versus crisis and symptom,

which is the process that we're in now.

It's much cheaper to prevent and cure

than it is to manage a crisis or just simply manage the symptoms of disease.

Now, how are we doing in this process?

Well, there's something like twenty thousand gene targets,

meaning twenty thousand genes that encode for proteins;