MEDICINAL CHEMISTRY Homework 2 - ANSWERS

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1 MEDICIAL CEMISTY omework 2 - ASWES 1. eceptor binding curves. Make a plot of %drug-bound versus -log[drug] for a drug whose K D is 5 x 10-6 M. Make a plot of %drug-bound vs [drug] for this same system. To do this calculate %drug-bound at drug concentrations of 5 x 10-8 M, 5 x 10-7 M, 5 x 10-6 M, 5 x 10-5 M, and 5 x 10-4 M. To calculate % drug bound, use the equation that we have used previously (shown below). Are there advantages that you see for the plot using -log[drug]? 1/( K eq D free 1) = T free / T total ere are the plots: % Bound (esponse) % Bound (esponse) e0 1.00e e e-4 Concentration 4.00e e Log[Drug] 7 8 Advantages of the Log plot: Midpoint of the plot is K D for drug. Easily identified by inspection. Data for several different drugs could be placed on one graph and it would be easy to tell which drug binds better. 2. In Panel A (below) a plot of the % effect (response) versus the log of the natural substrate concentration for this receptor is given. In Panel B we have a similar plot, except we see the response produced by drug binding at this receptor. What is the general term that is used for the natural ligand of a receptor? There is a generic name or term given to a compound which elicits a response such as this. What is it? ow well does the drug bind to the receptor compared to the natural substrate? Be quantitative (what is the K D for the drug and the natural substrate?)

2 atural ligand for receptor is call the "autocoid" "Agonist" gives same type of response as the autocoid. In this example it appears that drug and autocoid have identical K D values. The K D value looks like about 1 x 10-8 M (midpoint of the curve). 3. In Panel C we see the response of the same receptor when a second drug, Drug 2, is given by itself. In Panel D we see the results of a set of experiments with Drug 2 and the natural substrate for this receptor. In the first experiment drug 2 is absent and we see the dose response from the substrate. In the next experiment Drug 2 is given at one dose along with variable doses of the substrate so as to produce the dose response curve. Similar experiments are done to produce the other curves at 2 and 3 times the initial Drug 2 dose. A generic name or term is given to a compound such as Drug 2 which produces this type of effect. What is it? Drugs that give this type of response are called "competitive antagonists". 4. Explain the mechanism of action of Drug 2 and how it produces the phenomena exhibited in panel D above. ormally, the autocoid binds to the receptor and activates the receptor. In this case the drug binds to the same site that the autocoid normally binds and blocks the ability of the autocoid to bind and activate the receptor. 5. In the development of cimetidine, the early bioassays employed histamine at concentrations sufficient to cause 50% activation of the 2 receptor. This assay was not capable of detecting that α-guanyl histamine was binding to the receptor as a partial agonist. Why not? Use mock data plots to illustrate your answer. They changed the assay conditions to use a histamine concentration that causes 80% activation of the receptor. This allowed them to see that α-guanyl histamine is a partial agonist. In fact, this assay highlights the fact that a partial agonist can be viewed as a partial antagonist. Again, use mock data plots to illustrate your answer. At istidine 50% concentrations the presence of a partial agonist that activates the receptor to ~50% will be invisible. At istidine 80% concentrations this same partial agonist will show up as a weak antagonist. This reveals that a partial agonist also can be viewed as a partial antagonist. Which property of the molecule that is observed depends upon the way that the assay is conducted.

3 Partial agonist alone Partial agonist added in the presence of "histidine-50%" Partial agonist added in the presence of "histidine-80%" % response 6. In the development of the drug Cimetidine, which is used to decrease acid secretion into the stomach, and prevent the discomfort of heartburn, acid reflux and pre-ulcerative conditions, the molecules tested had an imidazole group at one end of the molecule, and, among others, one of the three groups shown below at the other end of the molecule. S C C 3 C 3 C a. What was the rationale for including the imidazole ring? The natural ligand, histidine,contains an imidazole ring. In this case the autocoid served as the lead compound in drug discovery. b. Of the structures 1-3 shown above which is the most basic and why? In answering this question use words, resonance forms, etc. in your explanation. Which structure will be more easily protonated (at any given p)? The most basic is 2. In each case, you can draw the same resonance structure. So, what determines the basicity of the molecules is the electronegativity of. The more electronegative will be less basic. = is the least electronegative, thus 2 is the most basic. =1 or 2 x C 3 x C 3 x C 3 c. Which of the structures 1-3 was used in Cimetidine and what was the rationale for its inclusion? Structure 2 was used in cimetidine. ammett plots identified a QSA suggesting that this functional group might be effective.

4 7. What are two key properties of receptors that allow small doses of an appropriate drug to elicit a significant biological response. (I discussed these key features in our first lecture on receptors). eceptors SELECTIVELYbind an autocoid and AMPLIFY this signal. So, a single molecule of drug can block signal amplification (or activate a receptor resulting in an amplified signal). Thus, small amount of drug gives large effect due to amplification. 8. Consider the following situation. The natural ligand for a receptor has a K B of 1 x 10 6 M -1. A competitive antagonist for this receptor has a K B of 1 x 10 9 M -1. Biological studies show that activation of the receptor occurs at natural ligand concentration of about 1 x 10-6 M (1 µm). Under these conditions, what concentration of drug will be required to place 90% of the receptor in the drug-bound form (i.e. 90% of the receptor is "blocked")? (We derived the necessary equations in class). We derived the following relationship in lecture [ec Drug]/[ec Autocoid] = (K Bdrug [Drug])/(K Bautocoid [Autocoid]) 90/10 = (1 x 10 9 M -1 [])/(1 x 10 6 M -1 [1 x 10-6 M]) =9 x 10-9 M (9 nm drug is required) 9. Does cimetidine adhere to Lipinki s rules? MW = 252.3; -bond donors = 3; -bond acceptors = 7; Log P = 0.4, free-rotating bonds = 7. one of these parameters violate Lipinskiʼs rules. Thus, the rules predict that the drug will be OK with respect to bioavailability. 10. Given information about the IC 50 of the drug and the concentrations and binding properties of the autocoid it is possible to calculate the K i for the drug. From the Ki is possible to calulcate the ligand efficiency. The equation relating K i to IC 50 can be written: Plugging in the numbers given in the problem (for K M insert the K D of histamine for binding at the 2 receptor) we can calculate that K i = 1.5 x 10-8 M. Using the equation DG = TlnK eq where, at 25 C, T = 0.59 kcal/mol, we can calculate that the free energy of cimetidine binding to the 2 receptor is about 10.6 kcal/mol (make sure you convert K D to K B for use in this calculation). Ligand efficiency, Δg = 10.6 kcal/mol / 17 atoms = 0.62 kcal/mol/atom.

5 11. Why did addition of a -C 3 and a -OC 3 group make the pyridine ring in omeprazole more basic? Why does this structural feature help omeprazole accumulate inside acidic compartments of the stomach-acid producing parietal cells? (int: draw the rxn in question the protonation of the pyridine ring. Then use resonance structures to consider how substituents on the pyridine ring affect the stability of the compound on each side of the equation that is, how substituents alter the equilibrium of the reaction). The unprotonated pyridine is lipophilic and easily crosses membranes (into acidic compartments). Once inside an acid compartment the pyridine ring is protonated. This makes the molecule charged and very hydrophilic, thus unable to cross membranes and escape the acidic compartment. Any electron-donating substitutent will increase the basicity of the pyridine ring. Look at a table of ammett substituent constants (sigma, σ) to find other electron donating substituents. 12. Suggest two other substituents that would have a similar effect on the basicity of the pyridine ring found in omeprazole. Try - 2 and -C 2 C 3 ammett tables tell us that these are electron-donating. 13. Imagine that you have been placed in charge of a drug-development team with the goal of developing a receptor antagonist. There are no known lead compounds. What would you use as the lead compound? (ote: this is a general question you do not need to know anything about the structure of the natural ligand for the target receptor.). Could you use a similar strategy in the design of a reversible enzyme inhibitor? Use the structure of the natural ligand, the autocoid, as a starting point ("lead") for drug discovery.