Serendipity And Drug Discovery

Question 0

What are the main examples of drug compounds discovered by serendipity ?

Answer 0

Penicillin
Cis-platin
Viagra

Question 1

What is an example of an aspect of the drug discovery process which still relies in serendipity?

Answer 1

Screening compounds

Question 2

How was cisplatin discovered?

Answer 2

An experiment was conducted using platinum electrodes to study the effects of electrical fields on the growth of E. coli. It was found that that this caused inhibition of cell growth.

Cisplatin is now used as an anticancer agent

Question 3

How was Viagra discovered?

Answer 3

Originally developed as a treatment of angina and high blood pressure,
During clinical trials it was found that men did not return unused tablets,
Further investigation revealed a mechanism of action leading to Viagra being marketed as an anti impotence drug.

Question 4

What is combinatorial chemistry?

Answer 4

A new methodology for synthesis which allows for the rapid synthesis of molecularly diverse compounds for biological testing.
This was developed as synthetic chemists could not supply enough compounds to keep the bioassays running efficiently (following the introduction of HTS which allowed bioassays to be performed on 10,000 compounds per month!)

Question 5

What is iterative drug synthesis?

Answer 5

Individual drug synthesis.

This is very slow

Question 6

What is the advantage of combinatorial chemistry?

Answer 6

We can take a shortcut in the biological testing process by combining pure compounds to give mixtures and simply testing the mixture, thus substantially saving time as it is much easier to perform a biological assay on 1 mixture of 1000 compounds than 1000 individual bioassays. This saves both time and money in the discovery of new drugs

Question 7

What is combinatorial chemistry based on?

Answer 7

The notion that compounds should be synthesised and biologically evaluated as mixtures

Question 8

What is the criterial of combinatorial chemistry?

Answer 8

Im just be reliable as we are trusting the making of chemical bonds

Question 9

What is the process of combinatorial chemistry compared to iterative method in the making using 3 different amines and 3 different acid chlorides?

Answer 9

The iterative method would require preparation of the amides one at a time followed by purification and testing each one individually in the bioassay.
This may require 1 day to make each of the, totalling 9 days as there are 9 products. If you were mass producing 1 million analogues, this would take too long.

In the combinatorial method, we take a mixture of amides and react it with another mixture of acid chlorides to give a mixture of products (termed a library) this would produce a library of 9 amides which can be tested for biological activity. This means that instead of doing 9 separate syntheses we only have to do 1

Question 10

What are some problems associated with the mixed reagent (combinatorial) method?

Answer 10

Dilution effects
Unreactive reagents
Synergism

Question 11

What are dilution effects?

Answer 11

The activity of an active compound would be diluted by inactive components in the mixture therefore you would need to consider these effects.
With bigger matrices, the number of books in your library increases exponentially. Dilution effects would then become a major issue

Question 12

Why is unreactive agents a problem with combinatorial chemistry?

Answer 12

Unreactive agents can lead to some books being missing.
There may be selective coupling of certain sets of ragents due to kinetics.

If all reagents do not to react then care must be taken to remove these chemicals otherwise you will be biologically testing reagents as well.
Thus, purification becomes difficult the larger the size of library we try to make

Question 13

Why is synergism or inhibition a problem when it comes to combinatorial chemistry?

Answer 13

Some compounds may interact with each other in the bioassay so that the combination is active but individual compounds are not.

Similarly, one compound may oppose another compounds activity leading to a false negative

Question 14

What is deconvolution?

Answer 14

The process of Identifying the active compound.

Question 15

What is the main aim of deconvolution process?

Answer 15

To do as few reactions and tests as possible

Question 16

How is the deconvolution process carried out using the library indexing method

Answer 16

Rather than making one big library containing all 9 compounds you prepare multiple sub libraries in which you hold one part of the molecule constant. (An indexed library)

E.g. A1 with B(1-3) 
Then A2 with B(1-3)
Then A3 with B(1-3)
Then start reacting B1 with A(1-3)
Etc. this gives 6 sub libraries. We can then test each of these 6 sub libraries against our bioassay to determine the active component easily

Question 17

Why is the library indexing method of deconvolution preferred?

Answer 17

We can test the sub libraries against our bioassay to determine the active component quite easily.

E.g. If two sub-libraries are found to be active, a table can be drawn and where the two sub libraries intersect will determine which compounds are active. This can be re tested by making more of the compounds,

Question 18

What is the deletion strategy of sub library synthesis?

Answer 18

Involves removing one or more of starting materials from the mixture synthesis and test for biological activity.

Only the mixtures showing activity would be resynthesised leaving out one or more of the acid chlorides (one type of reagent)

This new mixture containing deletion a would then be tested for activity, if activity is observed it shows the acid chlorides were not essential for activity.

By process of elimination we can determine active molecule without synthesise and testing all individual compounds in the original library.

Question 19

What is the main advantage of the deconvolution methods?

Answer 19

You do not need to synthesise all of the compounds of the target library to deduce which members of the library are active

Question 20

What are the two main methods of deconvolution?

Answer 20

Library indexing method (to form sub libraries)
Deletion strategy (process of elimination)

Question 21

What is a major problem with deconvolution?

Answer 21

This arises when more than one active compound is detected.
The only way to solve this is to go back into the lab to find out if they are all active through re synthesis and re screening

Question 22

What is one way of addressing some problems with making a mixture of compounds using conventional solution phase chemistry?

Answer 22

Move to solid phase chemistry

This is used for peptide/protein synthesis,
DNA and sugar chemistry

Question 23

What are the disadvantages of solution phase synthesis?

Answer 23

Each individual compound is made step by step on the gram scale, each step requiring mg about a day with work up and purification steps, thus extremely inefficient at producing a wide range of diverse structures through HTS

Question 24

What is the solid phase synthesis carried out with?

Answer 24

Synthesis is commonly carried out with a solid insoluble polymer (functionalised polystyrene bead)

Question 25

How is solid phase organic synthesis carried out?

Answer 25

Polystyrene is functionalised to give a chemically reactive attachment point. (In the case of merrifield resin this is a chloromethyl group)

A substrate is added to the attachment point

Reactions are carried out on the substrate attached to the resin. After each reaction the product is purified by washing the beads

The final product is cleaved from the resin bead, leading to synthesis of the pure product

Question 26

What are the advantages of solid phase organic synthesis?

Answer 26

Ease of handling
Ease of purification
One compound per bead

Question 27

What are the disadvantages of solid phase organic synthesis?

Answer 27

Expensive resin specialised equipment
Not all reactions are compatible with SPOS (grignard not compatible)
Chemist to carry out SPOS would need training

Question 28

What is parallel solid phase organic synthesis?

Answer 28

Where solid phase organic synthesis is used to prepare compounds in the same way we do in solution.

This produces a single reaction product in each action vessel but uses solid phase support as the medium.

E.g. The preparation of benzodiazepine libraries for the discovery of new human tranquillisers

Question 29

What is mix and split synthesis?

Answer 29

An alternative use of solid phase organic synthesis where individual pools of compounds are made by coupling one type of reagent to ute polymer bead in separate flasks.

These pure compound polymer beads are mixed together and divided into pools to give the starting material for the next coupling reaction to reagent B

This process of mixing, splitting and reacting can continue for many steps

Question 30

How is solid phase organic synthesis deconvoluted?

Answer 30

There are two main ways:
Micro manipulation and
Recursive deconvolution aka iterative resynthesis

Question 31

What is micromanipulaiton?

Answer 31

A way of deconvoluting solid phase organic synthesis
As each resin bead has only a single compound attached, in theory we can test the compound “on bead” (while it’s still attached), or we can test the compound by “partial cleavage” (release some of the compound on the bead for biological testing the usual way).

If the compound on a certain bead was active, then the rest of the he compound on the bead can be released to allow structure determination by NMR, IR, MS, etc

Question 32

What is recursive deconvolution?

Answer 32

This is the other form of deconvolution of solid organic phase synthesis.

You can set aside small portions after each step and before each mix to test the sub libraries.
E.g. If sample containing A1B2, A2B2 and A3B2 was active then we would know B2 is definitely present in our active compound.
We can then take the other reagent bound resin samples and react each with B2. Testing each of these will reveal the active compound.

The advantages of this technique becomes apparent when we prepare libraries comprised of millions of compounds