This is how I remember my exam. I am really bad with using the correct terms in the correct situations, so sometimes my answers are not 100% correct (e.g. in the first question, drugability has nothing to do with therapeutic effect). However, the atmosphere was relaxed and there were no weird silences or so. Good luck with

What is understood by the term drugability?
- The ability of a target to be modulated and produce a therapeutic effect, or rather it has structural components that can interact with a druglike molecule.
What is a drug-like molecule?
- It is small and organic, although there are also bigger molecules, like natural ligands
What is small?
- Smaller than 500Da
Why does everyone pick 500Da?
- Because of the Lipinski rule of 5
What is the Lipinski rule of 5?
- It means that if two of the aspects apply, the molecule is unlikely to be a good drug (not the best answer..). The rules are: more than 500Da, logP of more than 5, more than 5 H-bond donors and more than 10 H-bon acceptors.
And what exactly does it mean if two of these rules can be ticked? What was Lipinski famous for?
- Oh, for oral bioavailability.
Correct. Now you mentioned natural ligands. What are advantages and disadvantages of working with natural ligands?
- Advantage that you know that it can bind to the target. Disadvantage that it is big and complex and therefore has a lot of metabolites that need to be characterised and that could be toxic. Also, synthesis is more complex and therefore more expensive. So you usually try to make the molecules smaller.
Ok. We saw a lot of complex structures like taxol, penicilline etc and there it wasn’t a problem.
- Yes, because they are done semi-synthetically and you start with a smaller molecule.
So it is actually not true that the synthesis is a disadvantage.
- It is still more expensive and a longer process.


Now we’ll talk about cholinergic systems. What can you tell me about cholinergic receptors?
- There are two types, the muscarinic and the nicotinic receptors and their natural agonist is acetylcholine.
What does acetylcholine do?
- I mean the effect depends on the receptor it interacts. If it binds to a muscarinic receptor which is a GPCR, it will induce signalling pathways in the cell and if it binds to nicotinic receptors which are ion channels, it will open these.
He then showed me the structures of nicotine, muscarine, choline, acetyl CoA and acetylcholine and asked me what the first two structures were (nicotine and muscarine). What is the role of choline?
- It is the substrate for the reaction with Acetyl CoA to form acetylcholine.
And what is the metabolism of acetylcholine?
- It’s done by the acetylcholinesterase and acetylcholine is cleaved into choline and acetyl.
What kind of reaction is it?
- It’s a hydrolysis.
Can you draw the mechanism?
- I started drawing it with Ser and His, but he interrupted me and said it was enough.
What is the mechanism?
- I talked about the catalytic triad with Ser, His, Glu and that His acts as base and gives the proton back for the reaction.
And how is the C-O bond broken in the last step? How is that catalysed?
- The electrons from the O- move and choline will be released.
Is an alcohol a good leaving group?
- No. But it is stabilised by interactions with the active site.
Then how is it catalysed?
- (Had no idea what he wanted to hear..)
It is an acid catalysis.
- Yes, that’s what I meant when saying that His still has a proton.
He then showed me a scheme of ACh in the receptor binding pocket. What interactions could there be with the acetyl group?
- H-bonds with the carbonyl group, with a cation in the enzyme, hydrophobic with the methyl group.
What hydrophobic interactions are there?
- Van der Waals, between C-H groups
What other effects do hydrophobic interactions have?
- Water is pushed away and can therefore increase the entropy.
How does affect the binding energy? Can you write down the equation?
- dG = dH-TdS
Does it also affect the enthalpy?
- Not really
What happens when the water is pushed away?
- Interactions are broken, but therefore others are reconstituted when water interacts with other water molecules
So it actually does have an effect on the enthalpy. Just because I don’t mention it in the lecture, it doesn’t mean that it doesn’t play a role. Is the effect positive or negative?
- Positive for the binding because water-water interactions are stronger.
He then showed me two molecules with an extra methyl group on ACh and asked me why this was done.
- To sterically hinder hydrolytical cleavage which would deactivate the drug.
Do both enantiomers have a therapeutic effect?
- Depends on the active site, but since they are 3D structures, they have different interactions and one might bind have higher affinity than the other one.
Which one would you say is better in this case?
- The one where the methyl group doesn’t bump into the aa side chains and that can maybe also interact with other hydrophobic residues.
He then explained me where the methyl group would be in the scheme with the active site from before (showed the wrong position first, confused me quite a lot) and how it would affect the binding and then the time was over.