Week 6 Dr. Greig: Where Do Drugs Come From (Parts 4-6) Flashcards
what do we use when we need a new drug but have no starting point?
use high-throughput screening
once we find a protein of interest via target validation, how do we find which chemicals might bind to that protein and change the proteins function? Manual way and implications
- obvious answer: look in our own storeroom of chemicals (library of compounds in the lab)
- test all of these chemicals against the protein to see which will bind to the target
- it is shown that around 10^60 compounds will bind to the protein and follow through the impossible challenge in the body as discussed last lecture
- but we cannot test all of these compounds bc we don’t have enough matter to create it or space to store these compounds
how are chemical space and biological space analogized? and how does this analogy show the problem in drug creation?
Drug-like chemical space can be regarded as a vast ocean (most of it unexplored), and biological space can be regarded as tiny islands scattered throughout this ocean.
only the chemicals around the biological island will react with it
problem:
how are we supposed to find the chemicals that react with the drug target (island) when its a huge ocean of compounds?
how has nature narrowed down our search in compounds that react with our desired drug target?
we have done past research which has shown what types of chemicals react with what type of targtes. nature has grouped these chemicals and targets together so that if have a target that for instance looks like histamine, we can look at these chemical libraries associated with histamine and guided by nature to see what types of chemicals may react with the histamine-like target.
however, what is the problem with natures guidance?
review
Problem is that we are now sifting through chemicals against targets for which we have nothing to guide us …targets labelled undruggable
what does high-throughput screening of chemical libraries do?
when we have all these chemicals, some of which may be undruggable, we just randomly test their effects on the target to see what it does.
for instance we may test the chemicals for their activity on
- an enzyme (does the chemical do anything to block the enzyme?)
- cells expressing receptor/pathway (does the chemical do anything to block the ligand from binding to its recptor and activating it?/prevent the activation of a pathway)
- or on model organisms (for ex. when testing antibiotics, does this antibiotic kill this model bacterium)
the rare chemicals that give a positive response are called “hits”
what are the two divisions of screens?
Target-based screening:
Known target, looking for chemicals that modulate target or pathway
Phenotypic screening: - only looking for desired effect – doesn’t care how it works just cares if it works:
* Can I kill my osteoclast?
* Can I kill the tuberculosis bacterium?
* Find active compound, then consider how it works
what is the difference in way of thinking from back in the golden age and now? particularly when it comes to screening
Back in the golden age of drug discovery, all we had was phenotypic screening as we didn’t have the required biology techniques or knowledge to do target-based screening
Some will argue that this is why we are now struggling and should just get back to finding drugs that work, instead of trying to understand the biology and mechanisms
what is the main goal of high-throughput screening?
Chemical libraries will be screened for their ability to modulate the target protein, or for their ability to cause a favourable cellular change. Narrow down the search for a druggable chemical
what does the setup and results look like for high- throughput screenings
- Protein or cells are added to each well.
- A different compound from your library is added to each well
- Complex assay components are added…. …a simple result is obtained
- test readout could be a simple color change
- we will know that the chemical has modulated or changed that target because that particular well will fluoresce
what is our assay targeting when it changes color in the well?
when we have a chemical that blocks a receptor, we can test if the downstream reactions simply blocked the target or if it actually stopped the activation (we want the latter)
For instance, if we had a calcium-sensing dye, that reacted with calcium to give a fluorescent compound, then that is an example of a simple assay which will tell us if the downstream reaction occured
If the downstream reactions are halted = no increase in fluorescence = the compound effectively interfered with the activation process rather than merely blocking the receptor.
are the assays complex
yes the assays are complex and make use of complex biology, but the test yields a simple result – mere color change
what is a good model for phenotypic screening
zebrafish embryos are tiny transparent and easily grown to use
they are larvae, so not animals thus ethical for drug discovery
they are also transparent so we can actually see the effects of the chemicals on embryo development and whether they effect the pathway of interest
what is in silico libraries and screening? what is a problem with screening though?
computational screenings that can test an enormous amt of products. we can just ask the computer to tell us what compound is the best for the target
the libraries are stored on a digital database
problem:
there are some false positives - not useful if we get so many products that may work instead of 10 that definitely work
what is fragment screening
rather than finding the perfect drug in a library or a compound that is similar enough, we instead try to find a small bit of the desired compound.
then with this we can put together all the different discovered bits to find the ideal match of a compound
what does the future of screening look like
will transition to in silico screening so we dont have to manually look through a library and conduct trials
instead we will find accurate compounds via computational power to find a starting point.
what does potency mean
how little a drug is required to have the desired effect
- how strongly a drug interacts with its target
how do we improve potency as we develop a drug
we have a starting point bioactive compound
- we insert it in the drug target and try to improve the potency by growing the drug to match exactly with the drug target
- for instance if a target has 4 pockets of space and the starting point fills one of them up, we would develop the starting point to fill all 4 pockets tightly for best interaction.
- with only 1 or 2 filled = poor potency
- with 3 or 4 filled = good potency
- essentially more/better binding interactions between evolving drug and target = improving potency
- the drug is trying to get a better “grip” on the receptor
the more potent a drug is the…?
- less likely it hits other targets (less toxic)
- less needed to dissolve (less for solubility)
- less you need it to be absorbed (permeability)
- less problems you have in the body – more effective
why can greater potency sometimes lead to better selectivity and avoid toxicity. use an example to explain
for example let’s say we have four drug targets, all very similar in shape but all have different properties.
inhibition to target A will cure epilepsy but inhibition to target B C or D will cause really bad side effects
if we have a drug that has low potency, it will have fewer binding properties, and will be able to fit in all of the targets. This means it will not be good enough to cure epilepsy, but at least the side effects wont occur because its not fully gripped on.
If we have a higher potency, we will have more binding interactions. we can grow the drug so it binds properly to target A to cure epilepsy, but not bind properly to the other targets, thus preventing side effects.
thus more potency led to selectivity and avoidance to toxicity!
what is on target toxicity? expand on epilepsy example
if we inhibit target A stopping epilepsy, but later we find target A is needed for normal brain function, we will decrease epilepsy but increase side effects
this trade off is known as on-target toxicity
this means improved potency will simply mean that the side-effects are also caused at a lower drug concentration
ex. cancer drugs are potent and have therapeutic and toxic effects at very low concentrations
what is pharmacaphore? what are electronic properties? how are they associated with another?
the pharmacophore is the parts of a structure on the hit compound (as identified via screening) that bind to the target on their 3D orientation.
ex. cocaine and procaine are very different structures but have the same pharmacophore
it is based on the electronic properties - target doesn’t care about the exact nature of the chemical group – only what it does
so if a substance has the same pharmacophore or the same electronic properties, they can both bind to the same associated target
how do we improve a compound?
1. simplification via modification
we take the starting compound and remove or modify each growth then check if it made a difference to the activity
so if we modify a compound and there is a…
loss of activity = essential to the chemical
no change in activity = not necessary to the structure thus can remove for simplification
how do we improve a compound?
2. structural extension
(increase potency abd selectivity)
structural extension of the compound to increase potency and find additional binding interactions
makes the molecule much better
structural extension can also increase selectivity.
for instance if we have two very similar receptors, but one is larger, the same non-selective drug may fit into both receptors, but if the drug is structurally extended, it may only now fit into the bigger receptor (selective)
