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MDD – progress test paper UNIVERSITY OF HERTFORDSHIRE

PROGRESS TEST PAPER

Session: THIS YEAR Semester: A SCHOOL OF LIFE & MEDICAL SCIENCES DEPARTMENT OF PHARMACY, PHARMACOLOGY AND POSTGRADUATE MEDICINE Pharmaceutical Science Module Code: 5LMS0059 Methods in Drug Design: PROGRESS TEST DURATION OF EXAM: 3 HOUR THE FOLLOWING IS PROVIDED FOR THIS EXAMINATION: ONE question paper ONE MCQ answer sheet ONE short answer book INSTRUCTIONS TO CANDIDATES: The examination paper is divided into two parts. Section A carries one third (66.7%) of the marks. Section B carries two thirds (33.0%) of the marks. Answer ALL the questions in Section A and any ONE questions from Section B. Section A consists of 20 multiple choice questions Mark your answer to each question against the corresponding number on the MCQ ANSWER SHEET. For example, if you think the answer to question 12 is [C] mark your answer as follows: 12 [A] [B] [C] [D] [E]. Use an HB pencil and make your mark like this NOT a  or X or O. Erase all errors thoroughly. If you choose more than one option for a question, you will receive NO marks for that question. Mark your exam number on the answer sheet. Indicate the module title and code on the sheet. Section B consists of one short answer question. Answer each question in a SEPARATE answer book.

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MDD – progress test paper Section A Answer ALL questions on the MCQ answer sheet provided. This section is worth two thirds (66.7%) of the marks for the examination. You are advised to spend approximately 40 minutes on this section. 1. Which compound is the most basic?

Answer c

2. Pyridine can be synthesised using the: a. Skraup synthesis b. Pictet-Spengler synthesis c. Hantzsch synthesis d. Friedlander synthesis e. Knorr synthesis

3. What is meant by a lead compound in medicinal chemistry? a. A compound that acts as the starting point for drug design and development b. A leading drug in a particular area of medicine c. A drug which is normally the first to be prescribed for a particular ailment d. A pharmacophore e. A plant that is used in traditional medicine

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MDD – progress test paper

4. Which is the most probable main product of the following reaction?

Answer a 5. Which of the following needs to be established before the search for a lead compound takes place? a. b. c. d. e.

The pharmacophore Structure-activity relationship A bioassay Patents Robotic testing

6. Which of the following is a synthetic opioid drug? a. Codeine b. Heroin c. Norbuprenorphine d. Pethidine e. Thebaine

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MDD – progress test paper 7. Which of the following is NOT true? a. b. c. d. e.

Natural products often have a higher degree of structural complexity than synthetic / “industry designed” drugs. The majority of market drugs are natural products or derived from natural product sources. The main development of corticosteroid-derived medicines began in the first half of the 20th Century. The anti-cancer drug Taxol can be commercially produced by semi-synthesis. The current drugs of last resort against multidrug resistant bacterial infections are peptidebased natural products.

8. Compound 1, below, has reached clinical trials as an anti-cancer drug. It inhibits an enzyme involved in cell signalling.

Which of the following statements correctly describe structural features and/or interactions that could be involved in the activity of Compound 1? Statement 1: Isomer-selective interaction of a chiral centre with the biological target Statement 2: Interactions with aromatic amino acid residues by π-stacking Statement 3: H-bonding with the target from three H-bond donor groups in Compound 1 Choose the correct answer from choices a) to e) below. a. b. c. d. e.

Statement 1 only is correct Statement 2 only is correct Statement 3 only is correct Statements 2 and 3 are correct Statements 1, 2 and 3 are all correct

9. Which of the following sets of atoms or ring systems are lists of isosteres? a. F, Cl, Br, I. b. SH, OH, SeH. c. CH3, NH2, OH.

d. e.

All of a., b. and c. are sets of isosteres.

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MDD – progress test paper

10. Which of the following relationships correctly relates IC50 to the inhibition constant Ki? a. IC50 = 2Ki b. IC50 = 0.5Ki c. IC50 = 1/Ki d. 1/IC50 = Ki e. None of answers (a.) to (d.) is correct

11. A competitive inhibitor: a. increases the Michaelis constant Km but does not affect the maximal velocity Vmax of an enzyme catalysed reaction. b. increases the maximal velocity Vmax but does not affect Michaelis constant Km of an enzyme catalysed reaction. c. increases both the Michaelis constant Km and the maximal velocity Vmax of an enzyme catalysed reaction with the ratio Km /Vmax being constant. d. increases both the Michaelis constant Km and the maximal velocity Vmax of an enzyme catalysed reaction with the ratio Km /Vmax varying. e. is not described by any of the above four statements.

12. Which of the following statements is INCORRECT when developing novel antimicrobials? a. The target enzyme is essential for the functioning of the cell. b. The target protein is often involved in microbial virulence. c. The target protein is never involved in microbial virulence. d. The target protein does not have homologous enzymes in the infected organism. e. Any novel drug should inhibit more than one enzyme in a metabolic pathway.

13. The structure of benzamide is given below. What is the correct SMILES string for the structure given?

Benzamide a. b. c. d. e.

nc(=o)c1ccccc1 NC(=O)C1CCCCC1 NC(=O)c1ccccc1 NC(=O)cc1cccc1 NC(=O)Cc1cccc1

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MDD – progress test paper

14. Which of the following structures arises from the following SMILES string?

CCc1cccc(CO)c1

a.

b.

c.

d.

e.

f.

(4th structure is the correct one)

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MDD – progress test paper

15. Which of the following is NOT one of Lipinski’s Rules of 5? a. Molecular Weight less than 500 Daltons b. Number of rings less than 5 c. Log P less than 5 d. Number of hydrogen bond donors less than 5 e. Number of hydrogen bond acceptors less than 10

16. Which of the following statements regarding the partition coefficient (logP) is FALSE? a. The standard organic phase used in the experimental calculation of logP is octan-1-ol. b. alogP is an in silico atom-based algorithm used to estimate logP. c. clogP is an in silico fragment-based algorithm used to estimate logP. d. For drug-like molecule alogP provides better predictions of lipophilicity than clogP. e. In silico predictions of logP are generally less accurate than experimental measures of logP.

17. Literature databases that can be used to retrieve scientific publications include a. MEDLINE and PDB. b. PubMED and PDB. c. MEDLINE and PubMED. d. PubMED and PSD. e. PSD and PDB.

18. The results of the screening of 15 compounds for their anticancer activity using a cell-based assay have shown that one of those compounds has exhibited high activity, while the other compounds were inactive. Which method would you choose for the further in silico studies to identify potential active molecules? a. Pharmacophore development b. Pharmacophore screening c. Molecular docking d. Molecular similarity search e. QSAR 19. Which of the following methods is NOT used for in silico drug discovery: a. Combinatorial chemistry b. Molecular docking c. Molecular similarity search d. Pharmacophore modelling e. Quantitative structure activity relationship (QSAR) 20. Molecular mechanics is used to calculate potential energy of molecular systems. Which of the following belong to non-bonded functional forms? a. Electrostatic and angle energy terms b. Torsional and van der Waals energy terms c. Bond and torsional energy terms d. Electrostatic and torsional energy terms e. Van der Waals and electrostatic energy terms

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MDD – progress test paper Section B Answer ONE question and write your answer in a separate answer book. This section is worth one third (33.3%) of the marks for the examination. You are advised to spend approximately 20 minutes on this section. .

Answer the following question 21. Propose a strategy to utilize molecular docking in virtual screening for molecules with possible anticancer activity from the database of natural products (40%). Provide a brief account on theoretical basis of molecular docking (40%) and list the challenges to docking approach in drug discovery (20%)

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