Medizinische Chemie I & II
10. August 2021


Introduction:


Tell me about what is a good drug
I explained how the structure should be considering Lipinski’s rule of 5. He wanted more general information and mentioned PK and PD. First he wanted me to explain everything that has to do with PK. I said ADMET and explained each. Absorption with Lipinskis rule of 5, oral bioavailability, Metabolism Phase I and II. He wanted to hear more about PK but I didn’t know what to add.
Then he started talking about PD and the interactions of a drug in its binding site
What leads to high binding affinity?
I said interactions between the amino acid residues of a target and the drug structure.
He asked why would a chemist want a drug not to be polar and orally bioavailable?
I answered that if you don’t want that it acts in the whole body, only where it was locally delivered. To reduce on-target toxicity (same receptors in other tissues)
What he wanted to hear: application of balms on the skin where it only acts in this area



Main thema: Cholinergic receptors

Q: Tell me about cholinergic receptors
A: There are nicotinic and muscarinic receptors with acetylcholine as natural ligand and nicotine and muscarine as agonists (i said antagonist but he corrected me and I explained why agonist is correct in this case)
He said muscarinic receptors are GPCRs and I said nicotinic receptors are ion channels
He asked what the two targets are
I said either the cholinergic receptors or acetylcholinesterase


He showed me the structure of acetylcholine in the acetylcholinesterase binding pocket
He wanted to know everything about the binding interactions at the positive N-atom.
I said ionic interactions with either glutamic or aspartic acid but also cation-pi interactions
He showed me the amino acid structures and wanted to know which amino acid (Phenylalanin, Tyrosin, Histidin) can provide the strongest cation-pi interactions.
I did not know but then we discussed about the hydroxyl group on tyrosine and he helped me with this but the final answer was that as hydroxyl is an electron donating group it pushes more electrons into the aromatic ring leading to a higher electron density and thus to a stronger cation-pi binding.

Then he showed me the structure of apixaban (anticoagulant) and wanted to know what happens in the metabolism.
I first saw the ether group which I said would be demethylated to the hydroxyl by Cyp450 (Phase I metabolism)
Then I started talking about the amides but I thought they would rather not be metabolised because you need harsh conditions to hydrolyse amides but he said this is only a problem in the lab but not in vivo. Then he asked me how many amides there are. Three. He said it was very likely that metabolism at the amides happen.
He wanted to know more metabolism. I said maybe oxidation at the aromatic ring which could be stopped by introducing a fluoride as bioisoster. He asked where? (ortho, meta, para to the ether) I said normally para but not possible because there is already a bond at this place so I said ortho. He was happy with this answer but asked what could be problems after introducing a F-atom. I said maybe the demethylase could not interact properly because of steric hindrance but this was not correct because F is rather small. He wanted me to say sth about cation-pi interactions (again) and I said they would be less strong as fluor is a sigma acceptor and removes electron density from the ring. This was correct (if there would be cation-pi interactions at all)

Gerade Prüfung gehabt.

Einstieg:
Q: Tell me all you know about hight throughput screening. How it is made and what it is used for.
A: Erst erklärt wegen den molekülen in der library, geräte etc. Er ritt recht auf dennTargets rum. What are you doing with the targets, how do you know which one is the best one? How do you find the best ones if you have 1000 compounds on your excel sheet etc. Bin nicht drauf gekommen was er genau wollte. Im Endeffekt etwas mit dem Pharmacophore und den Substituenten.

Q: What is a second messenger.
A: Hab keine Definition gesagt sondern einfach als Bsp. cAMP genannt. Musste es zeichnen. War dann ok.

Q: Does a structure always need to be water soluble
A: no
Q: why?
A: Steroids for example are poor water soluble --> applied on skin. War dann auch ok und weiter.

Q: Apixaban. Do you know what it is used for?
A: Antikoagulans
Q: do you know how it works.
A: Thrombozytenhemmer? --> No is a factor X inhibitor.

Und dann wie bereits beschrieben mit dem Metabolismus. Hall hat bei mir mehr selber gereded als ich. Hab einfach genickt. Hab dann noch paar vorschläge gemacht aber die schienen Chemisch nicht so wirklich eine gute Idee gewesen zu sein aber er erklärte dann wieso nicht.

Bei mir waren beide Teile etwa gleich lang. Ein wirkliches Hauptthema hatte ich nicht. Beim HTS mit dem Pharmacophore hab ich - obwohl er mir helfen musste - dann einfach zu dem Zeigs dass er mir gesagt hat noch Dinge gesagt, die mir grad eingefallen sind.

Vorbemerkungen:
Ich habe versucht, so vollständig wie möglich, meine Prüfung zusammenzufassen. Gut möglich, dass ich etwas vergessen oder vertauscht habe. Die Richtigkeit der Antworten kann ich auch nicht garantieren ;)
Ich habe die Prüfung in Englisch gehalten, habe aber das Protokoll übersetzt.

Seine Fragen sind in Normal, meine in [i]kursiv[/i], Sinngemässe/Original-Wiedergaben in "Anführungszeichen".


-----------------
Zuerst einige Erklärungen wie die Prüfung abläuft und (wie immer), dass es mehr eine Diskussion sein sollte. Er fragte auch noch was ich studiere (Interdis Bio-N), keine Ahnung ob dies einen Einfluss auf die Prüfung hat. Dann gings los.
________________________________
Dann begann er damit, dass Medikamente oft Carbonsäuren (R-COOH) und/oder Amine (R-NH2) enthalten, ich sollte erklären warum.
[i]Ich erzählte, dass Naturstoffe hauptsächlich auf C, N, O und H basieren und da Medikamente diese imitieren, jene Atome und funktionelle Gruppen folglich auch in Medikamenten auftreten müssen. [/i]
Er nickte und sah aus als wolle er mehr hören...
[i]Ich erklärte weiter, dass N und O die Polarität eines Wirkstoffes erhöhen, was für die Verteilung notwendig sei. Weiter sei bei einem physiologischen pH die COOH-Gruppe deprotoniert und die NH2-Gruppe protoniert, was die Polarität weiter erhöht und auch Interaktionen ermöglicht.[/i]
Er fragte warum Polarität wichtig sei.
[i]Blut (was ja bekanntlich wasserbasiert ist) ist das Transportmedium also muss eine gewisse Polarität für den Transport vorliegen.[/i]
Er fragte weiter warum genau COOH und NH2
[i]Langsam gingen mir die Antworten aus, also versuchte ich auf Rezeptorinteraktion zu gehen.[/i]
Er wollte wissen welche Interaktionen besonders wichtig sind.
[i]Ich begann mit dem Runterrattern von allen möglichen Interaktionen (H-Bonds, Dipol-Dipol etc...) [/i]
Er: Und welche sind die Wichtigsten für Rezeptorinteraktion....? ("Go through the list")
[i]Ich (langsam echt nicht mehr sicher), najaaaaa ääähhhmmm H-Brücken..., ("as I told you before..."[/i]
"Yes, but the charge you have, the strong charge-charge..."
[i]"Ah that's what you mean..." ich habe eigentlich mit Deprotonierung und Polarität genau das gemeint, "are those not polar and H-Bond - Charge Interactions?"[/i]
"Ah yeah true but those are the most important"

----- Damit war die Minieinführung erledigt -------

So, was machen gute Drugs aus?
[i] Begann listenartig: Affinity, Selectivity, Meta... *Unterbruch (-.-)* [/i]
"Good you mentioned selectivity" wieso ist selectivity so wichtig?
[i]Man möchte ja nicht, dass ein Medikament, beispielsweise bei GPCR, alle jene Rezeptoren blockiert, das wäre bei ubiquitären Enzymen hochproblematisch [/i]
Gut, ja das stimmt, gibt es auch Situationen, in denen Sie wollen, dass auch Familymembers betroffen werden?
[i](Shit, das habe ich nicht erwartet), Gut ja, äähm gibt es, zum Beispiel ähm, *nachdenken intensifies* manchmal möchte man alle Rezeptoren einer Familie weitgehend blockieren, um die Wirkung zu verstärken. [/i]
Gut vlt nicht alle aber es gibt ein ganz wichtiges Beispiel aus der Vorlesung, ich denke Sie haben ganz genau ein spezielles Beispiel im Kopf nicht?
[i](Jein, irgendwas schwirrte mir schon vor aber jaaaa xD) Gut ja das BCR-ABL Beispiel, für Tyrosinkinase in speziellen Krebsarten.[/i]
Gutes Beispiel, Was passiert da?
[i]Tyrosinkinasen sind überexprimiert, was problematisch ist, generell: Tyrosinkinasen Dimerisieren...[/i]
Jagut was dimerisiert?
[i]Tyrosin[/i]
Tyrosin ist eine Aminosäure, Sie meinen die Tyrosinkinase... Was passiert dann, wenn die dimerisiert?
[i]Es wird ein GPCR Mechanismus... *Hall schaut leicht komisch, mein Gehirn schaltet*, warten Sie nein dumm, die (auto)phosphoryliert dann im Zellinnern und... *Unterbruch*[/i]
Ja genau und dann wird die Signalkaskade ausgelöst. So nehmen Sie an, sie haben nun einen Tumor, den Sie bekämpfen wollen aber das Medikament ist Cardiotoxisch. Was können Chemiker nun tun?
[i]Naja Chemiker können nun versuchen vlt Bioistosters einzusetzen.[/i]
Naja, vlt können Sie das mal versuchen und hoffen, aber dann hat das ja auch Auswirkungen auf die Selektivität...
[i]Ja aber wenn Sie einen Krebs haben, kann man vlt eine etwas tiefere Selektivität in Kauf nehmen da die ja eh angegriffen werden aber dafür wird das Herz geschont. [/i]
Naja, aber was kann man tun, denken Sie daran, dass Chemiker nur wirklich wenig Möglichkeiten haben.
[i]Vlt Delivery Systems, eine Salbe oder Liposomen[/i]
Sie sprechen andere Darreichungsformen an, aber das ist auch nur begrenzt möglich, irgendwann sind da auch alle Möglichkeiten ausgeschöpft, was können CHEMIKER tun?
[i](Wieder total unsicher), Jagut eben Liposomen/Mizellen würden vlt ... *Unterbruch*[/i]
"CHEMISTS have very few options, they simply can modify and then pray to God that it works" (Ja merci xD)
[i]Jaguuuut, aber ist es nicht so, dass Tumore in der Angiogenese löchrige Blutgefässe (<200 nm) entwickeln, also man könnte das Arzneimittel in auf die Grösse eingestellte Liposomen verpacken somit könnte man vermutlich eine Akkumulation im Herzen verhindern und zu "Gunsten" vom Tumor verschieben. [/i]
Jagut wir wissen, dass Tumore andere Gewebe haben, da könnte man vielleicht etwas machen...
*Steht auf* Ich habe Ihnen hier eine Drug, deren Struktur Sie wahrscheinlich noch nie gesehen haben. Zeigt mir Apixaban (beschriftet), das Anticoagulans (sagte er mir) von vorherigen Prüfungen (juhuuu). Er erzählte mir, dass es neu sei und Milliarden generiert aktuell. Dann sagte er, ich soll mal beschreiben was ich so sehe, was da passieren kann.
[i](Ich habe mir die Struktur ja aus guter Hoffnung bereits angeschaut) Dann habe ich erzählt, dass wir Delta-Lactame haben, die eine Ringöffnung eingehen können. Benzolgruppen welche Oxidiert werden können. Relativ polar, da viele polare Gruppen. Eine Etherfunktion, welche an Codein erinnert, die zu R-OH metabolisiert wird.[/i]
Er nickte und sagte Ja, dann zeigte er auf das Carbonsäureamid und sagte, dass die Drug ja zugelassen sei, also Chemiker garantiert viel ausprobiert hätten. Dann wollte er wissen, was ich dort denke, was probiert hätte sein können.
[i]Ich sagte zuerst einfach aus Reflex, Bioisoster, er sagte jajaja aber was könnte man tun, ich sagte Ester, welcher zu einer Carbonsäure metabolisiert werden könnte, dieses würde dann deprotoniert und könnte eventuell stärker interagieren, falls das gewünscht sein würde. Dann wollte ich unbedingt noch sagen, dass man mit Fluor/Chlor noch die Benzolringe schützen könnte, kam aber nicht weit...[/i]

*Wecker klingelt*

____________________

Es gab noch einen kleinen Teil, bei welchem ich nicht mehr ganz weiss, wo er war. Jedenfalls im Raum "Selektivität" wollte er wissen, ob mit hoher selectivity off und on target toxicity verhindert wird.
[i]Off eher, on nicht, da das Target vlt auch sonst noch in pathways aktiv ist.[/i]
Dann sagte er noch, dass solche Toxizitäten für Projekte oft tödlich sei, warum.
[i]Naja giftige Medikamente bekommen keine Zulassung...[/i]
"Yeah, that's kind of obvious, isn't it?" Aber was könnte dann Konsequenzen und Möglichkeiten sein?
Dann gings weiter wie gehabt.

---------------- Ende des Prüfungsprotokolls -----------------

Generell gute Prüfungsstimmung. Er will echt genau etwas hören und beharrt solange darauf, bis man es sagt. Er hilft aber auch und versucht einem zu zeigen, worauf er hinaus will (manchmal nur nicht sehr erfolgreich).
Generell Fragt er meist seeehr Oberflächlich und geht dann in die Tiefe, wenn man etwas spezifisches erwähnt (wie die Tyrosinkinase bei mir).
Prüfungsprotokolle lernen hilft sehr...

11.08.2021 11.30
Medchem I&II

Q: Tell me about Hight throughput screening. How it is made and what it is used for.
A: It’s a method to find an appropriate lead for your target. You screen for millions of molecules. You have two different approaches: rationally and randomly. In the rationally you restrict your libraires whereas in the randomly you scan all the molecules.
Q: But how specific works the HTS?
A: I had no idea how it works specific, I only said: you have wells where you put first your target, then you put an agonist which can be fluorescent marked and then in every well you put a different molecule. When the right one binds to the target you have a signal (not really sure what he answered, he changed question…)
Q: You said there are millions of molecules where are the from?
A: …Database
Q: Yes, but they cost very much so where are they from?
A: …
Q: From natural product! What is the advantage and the disadvantage with natural product?
A: disadvantage: natural products are often very complicated structure so you have to simplify. Advantages: you can target also molecule that will not be drougable with normal molecules.
Q: True but normally you will not perform a HTS for molecules which are not drougable.
A: ...ok.


Q: Tell me what do you know about cholinergic receptor?
A: There are two different types, nicotinic is ion channel, muscarinic is GPCR.
Q: Acetylcholine will be hydrolyzed by acetylcholinesterase. Then he showed me the structure of acetylcholine in the acetylcholinesterase binding pocket. Where the esterase cleaves? And what is the function of serine?
A: it cleaves the ester group and serine make a nucleophilic attack.
Q: He showed me the structure of physostigmine and other acetylcholinesterase inhibitors.
Q: Can you draw the mechanism of inhibition?
A: I draw the mechanism (slide 41).
Q: What is the advantage for the structure of neostigmine and pyridostigmine?
A: Since the nitrogen is protonated, they will not pass the BBB and reduce side effect in the CNS:
Q: True, but also physostigmine has two nitrogen atoms.
A: I tried with maybe they are cleaved. (false 😉)
Q: The answer is that in physostigmine the nitrogen are only temporarily charged.


Q: Then he showed me a structure with the name (Palbociclib). I know you have never seen this structure. What can be?
A: It was a protein kinase since there was the typical aminopyrimidine group.
Q: What makes the aminopyrimidine group.?
A: It binds in the binding site where normally ATP can bind in kinases.
Q: It is possible that this molecule is a covalent inhibitor? and if yes which part of the molecule is the covalent inhibitor?
A: I had no idea…I tried with some group that seem to be reactive (like carbonyl, …)… sorry but I really didn’t understand his answer.
Q: About the group on the right (is a six member ring with N and NH), why the chemists add this group very often to the molecules?
A: Maybe the nitrogen atoms are reactive and can make some interactions in the active site.
Q: No, it’s not about pharmacodynamics.
A: mmm also for the pharmakokinetik.
Q: yes, because the nitrogen can be protonated an so it’s better soluble in water.
A: yes but so it pass the membrane difficult
Q: he answered it’s always a balance or something like that

The exam for me went as followed...

[b]What are drug- drug interactions?[/b]
Said something about cyp substrates and inducers but as I was really nervous I guess it didnt really make sense so he showed me a table of inducers/inhibitors/substrates and asked me to explain it with an example from the table.

[b]What is cAMP? What is it made from?[/b]
I said it is an intracellular signaling molecule (second messenger) and it was made from ATP. He asked how and I told him it was dephosphorylated in the cyclisation process.

[b]why are there often amine and carboxylic acid groups in drugs?[/b]
I said because they can from ionic interactions which are important for drug/traget interactions.

[b]he said correct but what other reasons are there?[/b]
I said that those two groups often occur in nature and therefore natural ligands often have those groups.

[b]Why is that good for a drug?[/b]
No idea what i said to that. Probably would have been good to say something about rational drug design.

[b]Can it be a disadvantage if a drug has those groups[/b]
I said something about too polar and they can not cross membranes (he corrected me and said "can cross membranes worse") and hydrolysis (which was not correct as I understood when i had to draw carboxyilic acid). So I dont know what he wanted from me. We moved on ...

[b]He showed me Metiamide (drug fro peptic ulcer) and asked about the functional group on the right. What is it called/what does it do ?[/b]
I am really bad at naming functional groups so i had nooooo idea (it was a thiourea group) but I said that it was for chain elongation. But he also wanted to hear that it substituted the guanyl group and lowered the pka therefore preventing an ionic interaction. I wish i had known that.

[b]Why are PPI better targets than H2 inhibitors?[/b]
Because they are further downstream in the pathway and therefore more specific. (he didnt seem really content with my answer but we moved on)

[b]Why is it good if a drug does not form metabolites?[/b]
I said that metabolites complicate a drug discovery process as they can have on/off target toxicity and complicate dosing, interindividual variation (fast/slow metabolisers) and then i explained how metabolites are found. By radioactive labelling -> animal models -> HPLC ->MS ->Synthesis of the metabolite and comparison.

[/b]Why does it need to be radioactively labelled?[/b]
So you can find it better. (that was enough for him i guess)

He then showed me the structure of Rivaroxaban. He pointed to the thiophene group.
[b]What is this functional group called?[/b]
Me: 0_0

[b]What interactions can it form?[/b]
I said H-bond acceptor.

[b]He was not happy with my answer but said that it in theory is possible so correct but if i look at the structure what do I see ?[/b]
I honestly didnt see anything... (He then told me that it is aromatic) and then it clicked for me and I said pi-pi interaction and kation-pi interactions.

[b]Do you know an amino acid that this could form an interaction with?[/b]
Phenylalanine

[b]What others do you know?[/b]
Phenylalanien/tyrosine/tryptohan

[b]Which one can form the best interaction? What did I say makes a good pi pi interaction?[/b]
He had to help me quite a lot but the answer was that the chloride next to the thiophene ring is an electron withdrawing group so the amino acide woul need an electron donating group. And the oxygen on the phenol ring is an electron donating group. ( I was confused at first and said but the oxygen is more electro negative so wouldnt it be a withdrawing group? he explained that because of its free electron the oxygen can from a double bond and be therefore donating.)

MedChem I & II
12.08.2021


NO GUARANTEE OF CORRECT ANSWERS

Mr. Hall is very relaxed, his goal is to have a discussion with you. Though if you drift too far from what he wants to hear he will tell you immediately. It's also rather based on understanding concepts than learning drugs by heart.

Hall: What does the term drug drug interaction say to you?
Talked about metabolism, enzyme family P450 and CYPs, especially CYP3A4

Hall: Why is it important?
side effects, toxicity, accumulation of substrates, danger for the patient

“he showed me a table of common substrates, inducers and inhibitors of CYPs”
Hall: What useful information can be seen in this table? Could you explain with an example.
Talked about Warfarin as a substrate and how the enzyme is inhibited by Cimetidine, leading to slow conversion of Warfarin and accumulation, possibly dangerous bc of limit of therapeutic window / toxicity

Hall: Cimetidine is on this table, what does Cimetidine bind?
I didn’t know, he said it was an H2 antagonist

Hall: What does an inhibitor do? Explain with the example of Cimetidine
Talked about how in competes with the natural ligand for binding but doesn’t lead to an induced fit and therefore there’s no cell signal.

Hall: What is the natural ligand of the H2-receptor? Can you draw me the structure?
Histamine

Hall: What effect do H2- inhibitors have in human?
Used for treatment against peptic ulcers as they inhibit gastric acid secretion in the stomach

Hall:*he showed me a picture of the slide with the HCl secretion inhibition, with H2, M3 and gastrin receptors*
Hall: Why is the proton pump a better target than the H2-receptor?
It is a more downstream signal, I said it has fewer side effects which he only partly agreed on. He talked about how there is no influence of M3, gastrin or H2 receptors if the proton pum is inhibited directly.

Hall: *showed a picture of PPIs*
I didn’t recognize them, although we just talked 5min about them. He said they are PPIs.

Hall: *picked one of the PPIs* This molecule is chiral. Where is it’s chiral center?
I didn’t find one, he said it was a trick question as the sulfur atom is chiral, having one double bond to the oxygen, on free electron pair and to more covalent bonds.

Hall: Why are racemic mixtures not desired?
I said most of the times only one of them is active.
Hall: Why?
*short (intense) silence*
Hall: because they have different 3D structures. DO you think this molecule has a big difference between the two enantiomers?
I said no because it’s rather small.
Hall: Yes, because either the oxygen point upwards or downwards, which does not make that big of a difference compared to larger drugs.

Hall: Histamine receptors are GPCRs. *He showed me the slide with the three different GPCRs and what their effect is*
Hall: What does this table tell you? Why is this useful for us?
Talked about different effects of different GPCR subtypes. He didn’t really like that answer.

Hall: There is a difference in H2 and H1 receptor, they signal differently.
Hall: *showed me three structures* Can you name these structures?
said IP2 & he nearly flipped, corrected myself to IP3.
The other two are Diacylglycerol and cAMP.

Hall: How is cAMP synthesized?
I said from ATP or AMP, not sure, anyway it is cyclysed by adenylylcyclase.

Hall: What is the nucleophile and what the electrophile in the reaction?
I just had to guess, had no idea
Hall: The hydroxy group on the ribose is the nucleophile and the diphosphate leaving group the electrophile (I’m really not sure if I remember this correctly though).

Hall: How can you differentiate between H1 and H2 antagonists?
I talked about how the active site is different and that drugs have different structures depending on what they are trying to inhibit.

Hall: How would you know that a drug binds the H2-receptor over the H1-receptor
I talked about crystallography but he said it’s difficult to crystallize GPCRs bc they are transmembrane molecules. so embedded in the membrane.
I don’t remember the exact answer to this question he gave me though.

Hall: What’s the difference between early and modern drug discovery?
early: target unknown, drugs just tested for their therapeutic effect
modern: target selection and validation first, screening for drugs afterwards

Hall: What’s one downside / risk of modern drug discovery as you just described?
I said that the target validation is a process taking place up until the clinical trials and that one can never be certain if the target is good until tests in human have been carried out.
Hall: What does that mean in regards of risks?
That a financial commitment / time must be invested but we can’t be really sure if the target is actually good.
He kind of didn’t like the answer but accepted it.

Hall: *showed me a picture of a drug* You have probably never seen this before
Nope
Hall: This is *talked about the drug but I don’t even remotely remember what it was*.
Hall: What special structural features does it have?
I said it has quiet a long alkyl chain

Hall: Yes. What does that mean?
It is hydrophobic
Hall: Yes. How do you think the drug is applied?
I said as a topically which he kind of agreed on but clearly wasn’t the answer he was after.

Hall: What is the problem if the drug is hydrophobic?
I said it is poorly soluble in the blood and will distribute quiet badly
Hall: How can we solve that?
Addition of polar groups

Hall: was kind of confused, I was as well
Hall: The alkyl group is a palmitate ester. A palmitate ester of a drug is often used as a prodrug . Why?
Because it is hydrophobic and helps the absorbing the drug in the stomach.
Then it finally clicked and I said after hydrolysis of the palmitate ester is more hydrophilic and therefore better soluble in the blood, leading to better distribution in the body.
He was relieved and I was as well.

Medicinal chemistry exam. 13.8.2021 at 10.30
Exam atmosphere is quite relaxed. At the beginning of the exam he explained to me that the goal is to have a conversation, so I can ask for help if I got stuck and I can't move forward. Not 100% sure that everything I wrote is correct!

Hall: What can you tell me about target validation.
Me: It a phase of drug discovery where the validity of a candidate target of the diseases is confirmed. For example, if during clinical trials is found that, when targeting a target, there is not the hoped physiological effect or any effect at all, then the target is not validated.
Hall: In the lecture we saw the example of the anticancer Imatinib. In this case, after some time patients developed resistance and the drug didn’t have a physiological effect anymore. Are you saying that this target is not valid?
Me: No of course. Then I would say that if targeting a receptor leads to a physiological effect, then the target is validated.
Hall: Oh, you are turning around things then [laughing]. What causes the emerge of resistance for drugs like these (referring to imatinib)?
Me: If there is a mutation in the binding pocket of the drug (which happens relatively fast in cancer cells due to their continuous cell division cycles) and for example some residues that forms a hydrophobic pocket mutate into a more polar or even charged amino acid, the binding affinity of the drug will be considerably reduced. Another example in the case of cancer cells is also when the overexpression of the receptor will make the drug activity vain (since you will need much higher concentrations to inhibit all the targets).
Hall: Yes, I see your point, what you are saying is all correct. In the first case you mentioned (the one with mutated residues in the binding pocket), how can you solve the problem of resistance?
Me: [Guessing] Maybe with crystallization of the mutated receptor you can see which residues are changed and you can modify your drug accordingly.
Hall: You’re confusing with another type of receptor, where co-crystallization was made.

Hall: [he showed me two structures] You have already seen one of these structures, while the other not. [The first one was a quite complex molecule with an 8-membered ring and many substitutions, I would say it was a pleuromutilin derivative. The second structure was Salvarsan]
Me: [not recognizing both structures] The first one reminds me of taxol since it has a similar 8-membered ring, but I’m not sure.
Hall: No this is not taxol, but what have in common with it?
Me: it is probably a natural product due to the complexity of the structure.
Hall: what can you tell me some disadvantages in design such type of structure as drug?
Me: Designing a complex compound is disadvantageous because it will increase time and cost efforts for the chemical synthesis on large scale.
Hall: This is true, but what can you tell me about morphine? It is also a complex molecule. Is it hard to produce too?
Me: no because it is a natural product.
Hall: and what about penicillin? Is it hard to produce penicillin on large scale?
Me: No because a semi-synthetic method is used.
Hall: then there is another major disadvantage of having complex structures, rather than production issue. Can you tell me what it is?
Me: Such large structures are also susceptible to many reactions of the metabolism, and this will complicate a lot the drug discovery project.
Hall: correct.

Hall: what about the second structure? What can you tell me?
Me: I don’t remember this structure.
Hall: It is an ancient antibacterial used to treat syphilis. What are the possible targets to treat a bacterial infection? Can you give some examples?
Me: Penicillins target the bacterial enzyme transpeptidase, which is responsible for the formation of bacterial cell wall.
Hall: correct.
Me: then also the bacterial genome can be targeted
Hall: Yes, but you already told me about the transpeptidase which is part of the bacterial genome.
Me: I can’t remember anything else in this moment…
Hall: You can target bacterial metabolism. We saw many examples in the lecture… What are the advantages and disadvantages of making a drug discovery on antibacterial compared to the drug discovery for example of an antipsychotic?
Me: Bacteria are very different organisms compared to host cells, so it would be easier to develop drugs that are effective just on bacterial cells and not also on eukaryotic host cells (cause fewer side effects).
Hall: Yes, this is a point, even if there are anyway many antibacterials which have many side effects. [It wasn’t what he wanted to hear. He said something like this:] Bacteria have a relatively small genome, therefore almost every protein is very important and can be used as target.

Hall: [Showed me the structure of clavulanic acid] What can you tell me about this structure?
Me: It is a beta-lactamase inhibitor.
Hall: How did you recognize it?
Me: It has the main ground structure as penicillins but it leaks the alpha-functionality, the functionality at C6 [pointing on the draw].
Hall: Correct. What can you tell me about this side? [pointing on the functionality at C3]
Me: [not so sure] Here in penicillins there is usually a double methylation functionality, while in this case we have a sp2 hybridized carbon.
Hall: Yes… well which functional group is this? [pointing towards the O4-C3-C8 centers]
Me: an enol
Hall: Yes. How is the reactivity of the enol?
Me: For example, it can do an Aldol reaction, Claisen condensation, or more in general it acts as a nucleophile so it will react with many different electrophiles (I mentioned carbonyls, alkylation, I wasn’t sure where he wanted me to go)
Hall: Well, we are going a bit too much into chemistry [laughing], I don’t think a Claisen condensation is very common in biological environment.

Hall: [Showed me the structure of a sulphonamide (the one on the left at p. 34 of the lecture slides)] What can you tell me about this drug? Which type of drug is it?
Me: It is a sulphonamide
Hall: How did you recognized it?
Me: Because it is a para-substituted aniline with a sulphone functionality.
Hall: Yes.

Hall: [Showed me a paper with a last structure. Sorry but I don’t remember the name. It had multiple functionalities: an oxime, a tertiary amine, a long alkyl chain connected with an ester bond, …]. You have never seen before this structure. It is an antipsychotic. This is a particular structure for a drug, can you tell me why?
Me: It has a long alkyl chain connected through an ester bond. This is probably cleaved in the blood since ester bond are labile and susceptible to esterases in the serum.
Hall: Why is this functional group useful for?
Me: Is makes the drug much more hydrophobic allowing adsorption in the gut, since it can pass through cell membranes.
Hall: Yes. What can you tell me about metabolic reactions that can occur on the structure?
Me: As already mentioned the esterase will cleave the ester bond. Then, probably the oxime and the tertiary amine will be oxidized.

Time ended

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.

Medchem exam, 16.08.21

Start Thema: Drugability and target interactions

Q: what's durability
A: I said when the target (protein receptors) has the right conformation to allow interaction with the drug
Q: tell me more about the interactions: what can you tell me about the pocket (size)
A: I was not sure about what he wanted to hear so I started talking about the structure in the space and the equality a drug must have to be good. Then we focused on the kinetic and he wanted me to explain that. I talked about solubility and wade me say "lipinsky rule" and explain it. I started with the MW which was the answer of its start question :D

Hauptthema: Cholinerge system
I was asked to tell something about the cholinerge system (muscarine and nicotine receptors) the he showed me some molecules and wanted me to recognise Ach and choline and make correlation (synthesis from choline to Ach). The he moves to what is esterase (what is cleaved mechanism with catalytic triade and specific role of the amino acid).
Then showed me some molecules and asked me what they are: they were Ach receptor inhibitors. I recognised Tropicamid so he asked me how. I told him from toxicology lesson ([smile]).
Then we changed molecules group again and we spent time talking about the differences at the molecules (they were Achesterase Inhibitors), we discussed about the amino groups charged and the one which were able to be protonated and why chemists prefers the first one: the answer was the ability not to pass the BBB.

I have heard so many difference about how Hall was during the exams... Conclusion: it depends on your experience! [smile] at my size he said he wanted a discussion and that was what we did! wish you good luck[grin]

Ich hatte die Prüfung am 16.8.2020 um 11:30

Einstiegsfrage: Warum haben so viele Medikamente Carboxyl und Amino Gruppen
Antwort: Sie sind sehr polar und daher gut bioavailable.
Fragt nach: wieso bioavailability und polarity wichtig sind
Ich: Das sie in das Blut aufgenommen werden, nicht ausfallen,... (er wollte aber einfach wissen das es die soluability erhöht)
Er: what else can you tell me about carboxylic acids and amino groups?
Ich: Sie sind auch an hydrogen bonding beteiligt.
Fragt nach: hydrogen bonding sind nicht die ersten Interaktionen die einem dazu in den Sinn kommen.
Ich: machen auch elektrostatische Interaktionen,
Er: warum machen sie elektrostatische Interaktionen?
Ich: können geladen sein, und dann machen sie die elektrostatischen Interaktionen
Er: Wann machen sie diese Interaktionen?
Ich: wenn das binding pocket auch eine geladene AA aufweist.
Er: aber von was hängt es ab ob sie geladen sind oder nicht?
Ich: pKa und pH. Ich sagte noch, dass eine Amino Gruppe einen pKa von 9 hat und die Carboxylgruppe einen von 4/5. (Ich wusste nicht auf was er aus will, er hat dann gefracht welchen pH unser Körper hat: 7.4 und ich sagte, dass es darauf an kommt in welchem Gewebe das Medikament ist ob die Gruppen geladen sind oder nicht. Ich weiss immer noch nicht was er bei dieser Frage genau hören wollte)

Ich musste Phenylalanin aufzeichnen

Frage: natürliche Produkte werden oft als lead genommen, was sind die Schwierigkeiten
Ich: Sind sehr komplex, schwierig zu synthetisieren.
Er: und wie umgeht man dies?
Ich: semisynthetische Vorgehensweise

Er: beschreibe HTS und auf was testet es?
Ich: Man hat eine library mit verschiedenen substances und schaut, welche Moleküle an das target binden. Man testet auf affinity und selectivity
Er: why does a drug have to be selective?
Ich: damit es keine off target toxicity gibt
Er: gibt es auch on target toxicity?
Ich: Ja
Er: beschreibe on und off target toxicity
Ich: off target: Nebenwirkungen aufgrund Bindung zu einem anderen target, on target: Nebenwirkung aufgrund Bindung an das eigentliche Target an in einem anderen Gewebe
Er: kann man durch HTS auch auf die Struktur schliessen?
Ich: Ja aber normal macht man es mit Cocristalisation
Er: wie kann man darauf schliessen
Ich: die Strukturen der hits vergleichen
Er: aber diese strukturen sind sehr verschieden. was ist ein pharmacophore
Ich: funktionelle Gruppen, die an der Bindung in die active site beteiligt sind, diese sollten bei den hits relativ ähnlich sein. Die auxophoren Gruppen unterscheiden sich
(Er war mit allem nicht so zufrieden, ich weiss nicht was die Antwort dazu gewesen wäre, wie man auf die Struktur schliessen kann)

Er: zeigt mir eine Struktur und will wissen wie sie Metabolisiert werden kann
Ich: durch Oxidation
Er: was kann oxidiert werden und zu was wird es? (-OH wird zu =OH, R-S-R wird zu R-S(=O)-R, er wollte natürlich die Namen der Funktionellen Gruppen wissen)

[b]Hauptthema: Antibiotika[/b]

Er: zeigte mir Salvarsan und ein anderes Antibiotikum und wollte wissen was es sind (waren unbeschriftet)
Ich: Antibiotika
Er: wieso
Ich: wusste nicht was sagen da sie keinen betalaktamase ring hatten und auch nicht wie cephalosporine aussahen
Er: was ist ungewöhnlich an der Struktur von Salvarsan
Ich: ist sehr symetrisch und die Bindung zwischen den aromatischen Ringen ist ungewöhnlich
Er: was ist das As?
Ich wusste es nicht und ratete eine AA, doch es war Arsen
Er: zeigte mir ein betalaktam inhibitor und wollte wissen was es ist
Ich: beta lactam inhibitor
Er: an was erkennt man es
ich: beta lactam ring
Er: was macht die beta lactamase
Ich: bacterien produzieren es damit die beta lactame nicht mehr wirken. die inhibitoren blockieren die beta lactamase, sodass die beta lactame wirken können (Er unterbrach mich, ich habe glaube ich zu viele ähnlich Wörter in einem Satz verwendet, dass man nicht mehr wusste was es soll. Er sagte einfach, dass die betalactamase den beta lactam ring spaltet.)

Er: Ich habe in den Vorlesungen 5 mechanismen gezeigt, an denen Antibiotika angreifen können
Ich: inhibition of cell membrane synthesis, transcription und protein formation (habe nur 3 sagen müssen da der Wecker dann klingelte)

Er: zeigt mir eine Struktur von einem Penicillin analogon und Fragt welche AA darin zu finden sind
Ich: Valine und Cysten (Er: ja immer, wenn ein schwefel darin ist, ist cystein beteiligt)

Fach: Medchem
Datum: 16.08.21

--------------------------------------------------

ging bei mir um Produgs und B-lactame

Hatte kein Hauptthema. Zuerst über PK und PD gesprochen dann ein wenig über Histamin und wie Ranitidin gefunden wurde (Guanidine mit Nitrogeuppe damit deprotoniert). Und zum Schluss hat er mir eine Struktur (gesagt ich hätte sie vermutlich noch nie gesehen) mit Fettsäureschwanz gegeben und gefragt warum dieser angefügt wurde.

17.08.2021

Er stellte die Fragen in Englisch, habe meistens auf Deutsch oder in einer Mischung geantwortet.

Introduction:
H: Ich habe Ihnen in der Vorlesung den Zeitstrahl von modern drug discovery gezeigt, erzählen Sie mir darüber.
I: Step by step alles dazu gesagt was mir eingefallen ist.
H: Was ist der Unterschied zu früher?
I: früher: drug das funktioniert, erst später den Mechanismus (mithilfe des Drugs) herausgefunden, heute: zuerst Mechanismus kennen, dann ein Drug dazu finden (HTS oder von natural ligand)
H: Wieso kommen starke Säuren und Basen oft vor/was sind ihre Vorteile?
I: machen polar -> gut für die Distribution mit Blut. und ionic interactions sind sehr wichtig (habe stark gesagt, er hat dann gefragt ob sie wirklich stark sind, ich so kommt auf die Entfernung an, er so nein sie sind schwach (non-covalent), es sind einfach die stärksten von den non-covalent, aber sie sind trotzdem schwach).
H: geben sie mir ein Beispiel für eine starke Säure.
I: Carboxylgruppe (weil ich etwas überlegt hatte, musste ich es schnell aufzeichnen)
H: Welche Aminosäuren interagieren mit Carboxylgruppen.
I: Lysine, Histidine, Arginine
H: Wieso ist mit Arginine die stärkste Interaktion)
I: wusste ich nicht, musste dann Arginine zeichnen und kamen dann auf H-bond -> kann mit COOH zwei H-bond bilden, das und die ionic interaction machen sie so "stark"

Antibacterials:
H: legte Blatt mit Penicillium G (beschriftet) hin und fragte was es ist?
I: Antibiotikum, inhibiert Transpeptidase,...
H: Was sind die drei Probleme, welche Chemiker damit haben?
I: Nicht säure-resistent, Resistenzbildung von Bakterien (beta-lactamase) und nicht effektiv gegen gram negative Bakterien. (bin nicht auf anhieb auf alle drei Punkte gekommen, er liess nicht locker bis ich alle sagte)
- dann noch kurz was über bulky-groups und dass es aus Valine und Cysteine hergestellt wird und dann war die Zeit rum.

Er wartet wirklich bis sein Stichwort fällt und lässt nicht locker, hilft aber falls man nicht direkt drauf kommt.
Noch als kleiner Tipp: Wiederholt ab und zu Stichworte, auch wenn ihr sie bei einer anderen Frage bereits gesagt habt. Ich habe darüber gesprochen, dass Bakterien Resistenzen gegen Penicillin entwickelt haben, zB beta-lactamase. Danach kam die Frage, welche Probleme Chemiker haben. Habe dann die Resistenz nicht mehr erwähnt, da ich ja davor darüber gesprochen habe. Er wartete aber so lange und bis ich darauf kam, dies nochmal zu erwähnen und erst dann ging er zur nächsten Frage.

Zuerst als Einführung drug discovery process.
Einfach frei alles dazu erzählen was man weiss. (basic research, target identification and validation, lead compound and improvement)
H: Was ist ein gutes Target?
A: kommt nur in kranker Zelle vor
H: Sonst noch?
A: Drugable
Irgendwie sind wir dann bei natürlichen compounds gelandet
H: Was sind Vor- und Nachteile?
A: komplex --> teuer herzustellen, semisynthetic approach. grosse Struktur --> viel Metabolismus. Metabolismus kann zu Toxizität führen und macht alles komplizierter
H: Ich wollte auch Vorteile hören!
A: binden vielleicht stärker als synthetische?
Irgendwie ging es dann weiter zu Stoffen welche mit der DNA interagieren als Beispiele für natürliche Stoffe
H: Nenne ein DNA intercalating Stoff
A: Tetracyclin
H: weiss nicht ob stimmt. (wühlt in Blätter rum, scheint nicht so als ob er findet was er sucht) Wird schon stimmen

Hauptteil: Antibiotikum
Zeigte Struktur von Cephalosporin mit beta-Lactam Inhibitor gekoppelt.
Zuerst einmal sagen um was es sich handelt
H: Wie wird es im Körper gespalten
A: Esterase (Ester-bond)
H: Was passiert wenn es ganz ins Bakterium aufgenommen wird?
A: Weiss nicht ob es Esterasen hat um es zu spalten
H: Weiss ich auch nicht. Aber unabhängig davon?
A: Beta-Laktam Inhibitor kann nicht wirken, ist inaktiv. Cephalosporin wird durch beta-lactamase inhibiert
H: Wenn man genügend hohe Dosis gibt, ist dies kein Problem. Wie funktioniert denn ein beta-Laktam Antibiotikum?
A: inhibiert Transpeptidase und damit cell wall synthesis
H: Und was passiert wenn es Transpeptidase bindet auf molekularem Level?
A: verstand nicht was er von mir wollte
H: Welche Teile der Struktur sind essenziell?
A: beta-Lactam Ring, COOH, NHO. Achso, Ser greift O von Lactam an und Ring wird geöffnet.
H: Und was weiter?
A: keine Ahnung
H: Wie unterscheiden sich Cephlasporine und Penicilline in ihrer Struktur?
A: Penicillin hat fünfring statt sechsring
H: Genau und Doppelbindung in Ring fehlt ebenfalls
A: stimmt
H: Also was passiert mit Doppelbindung nach Ringöffnung
A: delokalisierte Elektronen, werden verschoben
H: genau. Zeichne es auf
A: Musste einfach mal geöffneter beta-Lactam Ring zeichnen mit Sechsring dran
H: Wie werden Elektronen nun verschoben
A: Hatte keine Ahnung. Dachte vielleicht Richtung N
H: Nein N ist ja schon negativ. Welches Atom ist elektronenziehend
A: Ah, demfall Richtung O von Verbindungsstück zu beta-Laktam Inhibitor
Wecker klingelte
H: Genau
Und dann zeigte er noch, dass dann irgendwie Elektronen zur Ester-Bindung gehen und diese gespalten wird. Wirklich verstanden habe ich es nicht

Die Stimmung in der Prüfung war sehr angenehm und Hall versuchte immer zu helfen, wenn ich nicht weiter wusste
Beide Teile waren etwa gleich lang. Gab noch viele kleine Zwischenfragen, an welche ich mich nicht mehr erinnere. Vielfach versuchte ich das Thema in eine Richtung zu lenken, aber er unterbrach mich jedes mal und stelle eine andere Frage.