You must answer FOUR of the SIX questions. Use a SEPARATE answer book for EACH question.

Transcription

1 UNIVERSITY OF EAST ANGLIA School of Pharmacy Main Series UG Examination DRUG DESIGN AND MECHANISMS OF DRUG ACTION PHA-5001Y Time allowed: 2 hours You must answer FOUR of the SIX questions. Use a SEPARATE answer book for EACH question. This paper consists of 10 pages in total. Dictionaries are not permitted in this examination. Notes are not permitted in this examination. Do not turn over until you are told to do so by the Invigilator. Do not take this question paper out of the examinations room. (PHA-5001Y) Module Contact: Dr Zoë Waller, PHA Copyright of the University of East Anglia Version 1

2 2 1. Answer ALL parts (a) to (e). Saxagliptin is a covalent serine protease inhibitor used for the treatment of type-ii diabetes. The final step in the synthesis of saxagliptin is shown below. Below is an EI mass spectrum of the above reaction mixture before all of compound 1 has been converted to saxagliptin. (a) Identify the base peak and the peaks that represent the molecular ions of compound 1 and saxagliptin. [10%] (b) What does the m/z represent? [5%] (c) Explain the relative intensities of the peaks at m/z = 297 and 288. [25%] Question 1 continues...

3 3 question 1 continued. (d) Given below are the Rf values for this reaction mixture when analysed by normal phase TLC under three different elution conditions. (i) Which of these solvent systems is the most polar? Explain your answer. [10%] (ii) Calculate which of these solvent systems would be best suited for purifying a mixture of compound 1 and saxagliptin by column chromatography. Dichloromethane Hexane/Ethyl acetate (1:1) Ether Rf Rf Rf Compound Saxagliptin [30%] (e) Identify TWO advantages and TWO disadvantages of covalent inhibitors compared to competitive inhibitors. [20%] TURN OVER

4 4 2. Answer BOTH parts. (a) Fragment based approaches to drug design are gaining in popularity. (i) Explain, with the aid of diagrams, the concepts behind Fragment Evolution, Fragment Linking and Fragment Self-Assembly. [30%] (ii) What are the ideal properties of a fragment? [10%] (iii) Compare and contrast fragment based strategies and high throughput screening. [15%] (b) The 1 H NMR spectrum overleaf is of an amino acid. The spectrum has been run in the presence of D2O. (i) Showing all your reasoning, identify and name the amino acid from the NMR given. [30%] (ii) List the proton signals that have been removed from the spectrum due to the D2O shake and explain why this has occurred. [10%] (iii) Would you expect the amino acid to be fluorescent? Justify your answer. [5%] Question 2 continues

5 5 question 2 continued. TURN OVER

6 6 3. Answer ALL parts (a) to (d). Cetirizine and clemastine are both antihistamines. (a) Which of the two antihistamines would cross the blood brain barrier more readily? Your answer should include reference to specific functional groups in each molecule. [20%] (b) Compound 5 is an intermediate in the synthesis of cetirizine. A reaction scheme is given below: (i) Suggest reagents and reaction conditions for Steps 1-3. [15%] (ii) Suggest structures for intermediates 3 and 4. [10%] Question 2 continues

7 7 question 2 continued. (c) An alternative way to synthesise cetirizine intermediates involves the condensation of ketone 2 with substituted piperazine 6 in one step. (i) Provide the structure of the condensation product 7. [5%] (ii) Suggest reagents for this transformation. [5%] (iii) Draw the curly arrow mechanism for this transformation. [20%] (d) Although cetirizine is marketed as a racemate, the R-enantiomer of cetirizine is more active than the S-enantiomer. Using your knowledge about receptor binding sites explain how a receptor can discriminate between the TWO different enantiomers of cetirizine. Your answer should include a diagram of each isomer, the stereochemical assignments and an explanation of the types of interactions each functional group in the drug could have with the receptor binding site. [25%] TURN OVER

8 8 4. Answer ALL parts (a) to (f). The terphenyl 8 is used to target the B-cell lymphoma protein, BCl-XL. 8 (a) Describe how terphenyl 8 works. Your answer should include a description of the type of drug it is. [20%] (b) Draw the terphenyl 8 as you would expect it to exist at physiological ph [10%] (c) State the type of reaction you would need to form the bond indicated by the arrow. [5%] (d) In the development of terphenyl 8 you decide to use Protein-Ligand Docking. (i) Define Protein-Ligand Docking. [5%] (ii) Briefly describe the three different types of docking calculations. [30%] (e) Metabolites of terphenyl 8 are formed by CYP450. Justify how CYP450 enzymes are able to oxidise a wide range of drug molecules. [10%] (f) Suggest FOUR possible metabolic conversions that could occur for terphenyl 8. For each conversion highlight the part of the molecule at which the reaction will occur. [20%]

9 9 5. Answer ALL parts (a) to (d). Dacarbazine is a chemotherapeutic prodrug activated by metabolism in the liver. Below is a scheme for the synthesis and initial metabolism of the drug. (a) Discuss how you could monitor the reactions in step A by IR spectroscopy. You answer should include estimated positions of bands in wavenumbers. [10%] (b) Suggest a reagent for step B. [5%] (c) Provide a full mechanism for the formation of metabolite 9. Your answer should include a description of the catalytic cycle of a CYP450 enzyme. [60%] (d) Describe the mechanism of action of metabolite 9. [25%] TURN OVER

10 10 6. Answer ALL parts (a) to (e). This question is about statins. Lovastatin HMG-CoA (a) Statins are an example of a class of drug which are used in the clinic. Most drugs fail in the drug discovery process. Explain three reasons why drugs fail to reach the clinic. [30%] (b) The LogP of lovatatin is 4.3. Does it obey Lipinski s rules? Explain your answer. [20%] (c) Show the route to HMG-CoA from Acetyl-CoA, including the mechanistic pathway using curly arrows (you do not need to show the structure of CoA). [25%] (d) HMG-CoA reductase catalyses the next step in the synthesis of isopentyl pyrophosphate from acetyl-coa. The statins inhibit this step and are used in the control of cholesterol levels in humans. Explain how a statin can inhibit HMG-CoA reductase. [10%] (e) Statins are polyketide natural products. Show how phloroacetophenone is formed from poly-β-keto ester in the first steps of the polyketide biosynthetic pathway. [15%] END OF PAPER

11 School of Pharmacy Examination Feedback Summary Module Name DRUG DESIGN AND MECHANISMS OF DRUG ACTION Module Code PHA-5001Y Year 2016/17 Overall marks Mean mark: 52% Max. mark 80% Min. mark: 20% Grade distribution: 1 st Fail 2% 30% 32% 24% 12% Question: 1 No. of attempts 60 Comments: Parts (a & b): generally answered well. Most students understood the concepts of base peaks and molecular ions and were able to identify them within the mass spectra Part (c): some students were able to identify the structures associated with the fragments ions that were asked about, but many lost marks by not explaining why one fragment was more stable to the other and how this linked to peak abundance in the mass spectra. Part (d) (i) when asked about which was the most solvent system for the TLC data shown many confused polarity of solvent with polarity of the compounds (i.e polar compounds have smaller Rf, but polar solvents are better at eluting compounds up the plate, so a more polar solvent will increase the Rf of a compound on a normal phase TLC plate). Part (d) (ii): many answered this well and scored high marks. Many forgot that it is differences in CV values (not Rf values) that determines how well different compounds can be separeated/purified by column chromatography). Part (e): Many missed out lost of marks on this question. Much confusion over features of covalent inhibitors which were advantages and which were disadvantages. Many answers lacked the small amount of detail needed to clarify this. Question: 2 No. of attempts 21 Comments The responses to the question showed clear question spotting by students with the majority of answers failing to address Part A. As part A was worth 55% of the marks, even a near perfect Part B was not going to result in a pass mark for the question Part A (i) could be taken straight from notes. The question specifically asked for the cartoon diagrams presented in the lecture but the majority of students did not include diagrams; as they are asked for they form part of the marking scheme so were marks that were easily lost. Part A (ii) was better answered although many students forgot to include the two additional requirements of polar surface are and rotatable bonds. Part A (iii) was less well answered with few students providing more than bullet points. The question asks for compare and contrast and so requires some explanation. School of Pharmacy Summative exam feedback (V1) January 2013 Page 1 of 3

12 Part B. The NMR was well answered, although a number of students failed to spot that it was an aromatic compound. Part (ii) and (iii) were generally correct but lacking in detail on the explanation. Question: 3 No. of attempts 31 Comments: More than 80% of the students got >40% in my question. Although in general all of the students seem to understand the differences between molecules, functional groups and chemical elements, a few of them have indistinctively used these three terms. A similar scenario happened with the effect of lipophilicity/hydrophilicity/degree of ionisation at physiological ph on drug-molecule absorption, however the vast majority of the students seem to have the concepts really clear, some contradictory answers suggest that a few of them of them could be (slightly) confused. I was pleased to see that most of the students who attempted the reaction mechanism got it right. A number of the students did not use the wedge-dash notation required to represent 3D chemical structures but nearly all of those who did also assigned correctly the R,S configuration of the chiral carbon. Some students did not answer the receptor discrimination of enantiomers, perhaps due to time constraints as this is the last section of my question. I would like the students to bear in mind that all the functional groups in a molecule (not only the bulky ones or those at either end of the structure) could potentially interact with residues in the binding site, for example linking hydrocarbon chains. Question: 4 No. of attempts 45 Comments: a) Most students incorrectly identified the molecule as binding DNA it is a typical alphahelix mimetic, an inhibitor of a protein-protein interaction. b) Most students correctly drew the molecule correctly. A couple did not draw out the molecule in full and got only minimal credit for this c) Most students correctly identified the type of reaction as a cross-coupling d) Many students did not answer part d at all which indicates selective revision or question spotting - Two different types of answers were given by the students to define protein-ligand docking. Many students explained as the physical process of a ligand finding the place (binding site) on the protein surface to form the complex, and this answer was positively assessed. Nevertheless, the best assessed answer, given by a smaller number of students, was that defining docking as the calculations using computational resources to predict the orientation of a ligand in the binding pocket of a receptor. - In this case, many students seemed to misunderstand the question, in the sense that they were giving answers about Quantitative Structure Activity Relationships, which was not the topic of the question. A smaller number of students answered properly by simply School of Pharmacy Summative exam feedback (V1) January 2013 Page 2 of 3

13 stating the three types of docking calculations, i.e., including flexibility or not including it on the interacting molecules. Parts e and f, which were about metabolism were answered well. Part e most correctly stated that CYP450 has a large cavity and can accommodate a wide range of molecule types and sizes. Most students were very good at identifying the different positions where metabolism could occur. Most just stated phase 1, which was absolutely fine, but I was impressed that some also suggested phase 2 as well. Question: 5 No. of attempts 56 Comments: A generally well answered question with few fails. For part (a) Most people were able to suggest which bonds cloud be monitored as this reaction progressed. The best answers also included the wavenumbers off the bonds. Part (b) was probably the least well answered as many people thought this was a reduction reaction rather than a conjugate addition. Parts (c) and (d) were well answered. Most people have learned their mechanisms and were able to recall them under exam conditions. A few got a little lost with the final mechanism but no serious issues were found. Question: 6 No. of attempts 47 Comments: Parts a and b were answered almost perfectly in most cases. Unfortunately a lot of students only answered parts a and b which, again, indicates poor question choice/exam technique or avoiding revision of some topics. 6a) was looking for 3 explained reasons why drugs fail. The majority of answers were sufficiently detailed and well explained covering toxicity, efficacy and financial reasons with appropriate examples. 6b) was looking for an application of Lipinski s rules for the molecules. Again, most gave an excellent answer, stating each of Lipinski s rules and then applying this to the molecule. 6c) This was straight from the notes and involved the attack of acetyl-coa methyl group on a second acetyl-coa followed by a third attack on the resulting malonic ester. It was clear that very few people had bothered to revise this. When they had, they gained full marks. d) Given the two structures of HMG-CoA and lovastatin, it should have been clear that lovastatin is a prodrug and that the lactone structure in the inhibitor can open to form a structure that is very similar to HMG-CoA and can therefore bind to the reductase. This was only correctly answered by one person, but was covered several times across the lectures in DDMDA and others. e) This involved showing the pathway to phloroacetophenone from poly-beta-keto ester. It was quite poorly answered although several people scored full marks. School of Pharmacy Summative exam feedback (V1) January 2013 Page 3 of 3