Lecture 7 - Combinatorial Chemistry

Question 1

What is combinatorial chemistry and when is it used?

Answer 1

Simultaneous production of many compounds with defined structures in one reaction vessel, and then screening of the compounds in order to find one with the desired biological activity that can be used as a lead compound

Question 2

What is parallel synthesis and when is it used?

Answer 2

Simultaneous production of many compounds, each within its own reaction vessel. Generally used for structure optimisation rather than finding a lead compound

Question 3

What are the advantages of combinatorial chemistry over parallel synthesis?

Answer 3

Generates significantly more structures in a set period of time, therefore increases the chances of finding an active compound
Economically more efficient as no time is wasted carefully making each compound if none is a hit

Question 4

What are the disadvantages of combinatorial chemistry over parallel synthesis?

Answer 4

If one of the compounds in the mixture is a hit, structural determination is very difficult. If there is a false positive, lots of effort can be spent looking for an active compound that is not there
There is always a possibility that not all expected structures are created

Question 5

What is solid phase synthesis and when is it used?

Answer 5

A means of compound synthesis where the reactions are carried out using a starting material that is linked to a solid support
Used during combinatorial chemistry and parallel synthesis

Question 6

What are the 5 requirements of solid phase synthesis?

Answer 6

An insoluble polymeric support, such as a resin bead
A linker group covalently attached to the bead, which contains a functional group to which substrates can be added
A bond linking the substrate to the linker, that is stable to the reaction conditions (i.e. won’t break as more substrates are added)
A method of cleaving the produce from the linker
A method for protecting functional groups that are not involved in the reaction

Question 7

Name two linkers that can be used in solid phase synthesis to produce peptides

Answer 7

Wang-Resin Linker

Rink-Resin Linker

Question 8

Describe the process of solid phase synthesis using the Wang-Resin linker

Answer 8

React the linker with an amino acid that has the amine group protected
The OH of the linker and COOH of the amino acid react to form an ester bond
Remove the protective group on the amine
Add amino acids onto the now exposed amine
When complete, treat with TFA to detach the polypeptide

Question 9

Describe the process of solid phase synthesis using the Rink-Resin linker

Answer 9

React the linker with an amino acid
The NH on the linker and COOH on the amino acid react to form an amide bond
When complete, treat with TFA to detach the polypeptide

Question 10

What are the advantages of solid phase synthesis?

Answer 10

1. Excess reagents can be removed simply by washing with a solvent, as the final product is bound to a solid support
2. Easy removal of excess reagents means large excesses can be used, which drives the reaction to completion
3. Intermediates are bound to the bead so do not need to be purified
4. The support can be reused, as long as the product is cleaved off correctly
5. The process can be automated
6. As each product is attached to a bead, they can all be mixed together and each product separated at the end. This would be a disaster if done with solution chemistry
7. Can produce large quantities of compounds in a short period of time
8. Structures can sometimes have their biological activity tested while still attached to the bead

Question 11

What are the two methods for carrying out combinatorial chemistry?

Answer 11

Mix and Split method

Dynamic combinatorial chemistry

Question 12

What are the 3 methods for finding an active compound in a mixture following mix and split synthesis?

Answer 12

1. Micromanipulation - each bead separated and individually tested
2. Recursive deconvolution - some beads removed and tested at each stage of synthesis
3. Sequential release - the beads split up into smaller mixtures and each mixture tested (less beads to go through micromanipulation if one mixture gives a hit)

Question 13

What are the possible methods of structure determination once you have found an active compound?

Answer 13

1. NMR - although often not enough product is produced for this
2. Infrared - useful as doesn’t require the product to be released from the bead
3. Tagging method - each time a component is added to the growing a compound, a code is also attached to the linker on a different functional group. Acts like a barcode. Useful, but double the amount of chemistry involved

Question 14

What is dynamic combinatorial synthesis?

Answer 14

Combinatorial chemistry where the compounds are screened for biological activity in situ as they are synthesised

Question 15

How is dynamic combinatorial synthesis carried out?

Answer 15

Include the desired target in the reaction flask
Any active compounds bind to the target when formed
Reactions for generating compounds are reversible and compounds break down - unless they have bound to the target which removes them from the equilibrium
Freeze the equilibrium mixture to identify the active compounds

Question 16

What is a disadvantage of solid phase synthesis?

Answer 16

When assaying for biological activity, the resin bead can interfere and lead to false positives or false negatives, so it is best to remove the product from the bead first

Question 17

What is SPOS and when could it be used?

Answer 17

Solution phase organic synthesis

Can be used during parallel synthesis

Question 18

What is a pro and a con of SPOS?

Answer 18

Fewer steps and materials needed than solid phase synthesis
Extraction techniques are needed to separate the aqueous phase from the organic phase, such as a lollipop phase separator

Question 19

What are the two approaches to designing a lead compound?

Answer 19

Spider-like approach: A centroid or scaffold has many growing ‘arms’ of reactive functional groups
Fragment based lead discovery: Find epitopes (small molecules that bind to specific regions of the active site of the target) and link them together to form a compound

Question 20

What are the advantages of using the spider-like approach to designing a lead compound?

Answer 20

Increases the chances of finding a compound that will interact with the target site
Good chance the drug will have good oral bioavailability

Question 21

What are the challenges of using the spider-like approach to designing a lead compound?

Answer 21

Esters and other readily hydrolysed groups should be avoided

Need to avoid the functional groups gathering around one side of the scaffold (tadpole-like)

Question 22

What are the challenges of using the fragment-based approach to designing a lead compound?

Answer 22

Can be difficult to identify how the fragment has bound to the target
Can be difficult to link the fragments to form a viable compound

Question 23

What rules must each fragment in ‘fragment-based lead discovery’ obey if the resulting compound is to obey Lipinski’s rules?

Answer 23

1. MW < 300
2. Less than or equal to 3 H bond donors
3. Less than or equal to 3 H bond accepters
4. cLogP value less than or equal to 3
5. Less than or equal to 3 rotatable bonds
6. Polar surface area less than or equal to 60 angstroms squared