CHEM 4170 Problem Set #1

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1 CHEM 4170 Problem Set #1 0. Work problems 1-7 at the end of Chapter ne and problems 1, 3, 4, 5, 8, 10, 12, 17, 18, 19, 22, 24, and 25 at the end of Chapter Two and problem 1 at the end of Chapter Three in the textbook. 1. Why is the log P value of a drug important? (i.e. why is a balance of lipophilicity and hydrophilicity important?) 2. Use the log P table that I handed out in class to calculate either the log P for the given molecules or the πx for the given substituents. There are many correct answers so you must show how you calculated your values. (Explain: why can there be more than one correct answers?) A. E. H C C B. Br F. C C. G. Cl D. substituent

2 3. This example, highlights the fact that the principles of medicinal chemistry carry over into the field of toxicology. Compound "Z" shown below is highly toxic. Given the series of compounds and their biological activities, draw the pharmacophore for the toxicity first observed in "Z". By definition, the pharmacophore is the minimum structural unit that retains the biological activity in question. SH CH 3 CH 3 "Z" H CH 3 H toxic toxic toxic 4. Draw three analogs of aspirin, each containing a single bioisosteric substitution. C 2 H Aspirin 5. Though the concept of bioisosteric modifications was introduced as a method of choosing minor modifications on lead compounds, sometimes major changes in biological activity result from a bioisosteric modification. Discuss the possible reasons why a bioisosteric change in a lead compound could cause major changes in biological activity. Use a specific isosteric pair as an example. 6. What is the difference between pharmacokinetics and pharmacodynamics? Is pharmacokinetics or pharmacodynamics more important in drug design? 7. A chain homologation approach for the structural modification of aspirin (3) provided the compound shown below. This compound is a less effective analgesic than aspirin. Suggest possible reasons why. Propose analogs of aspirin that fit the other general categories of lead modification (in addition to chain homologation) that we discussed. C 2 H

3 8. Let's start this problem with a quick estimate for the volume of water in the human body: Assume an average human weighs 68 kilograms 70% is water; therefore this human contains about 48 kilograms of water. The specific gravity of water is 1 gm/ml, so remember that 1 kilogram of water (1000 gms) is one liter of water. Therefore, we can guess that an average human contains about 50 liters of water. I have no idea if this is exactly correct but we can use this value for our calculations and we'll learn something. ow, let's use this figure in a calculation. If a drug's binding constant (K B ) for its medicinal target is 1 x 10 6 M -1 calculate the dose required to block 90% of the biological target's function (dose required to ensure that 90% of the biological macromolecule is bound by drug). For these calculations, assume that the concentration of the biological target is very low relative to drug. Imagine that an improved analog has a K B of 1 x 10 9 M -1. ow, calculate the dose required to block 90% of the biological target. Hint: use the equation K b = [E I]/([E][I]) and that the concentration of free [I] is effectively a constant under these conditions. That is, the amount of [I] that you start with is not changed by the small amount of I that binds to E. 9. For a compound that has a K B of of 1 x 10 9 M -1 for a particular biological macromolecule (a) Calculate the concentration of drug required to achieve 50% binding of the target. (b) I showed you in lecture how to use the K B to calculate K D for this compound. Calculate the K D. Do you see an interesting, practical feature of the K D? 10. What is the hydrophobic effect and how is it relevant to drug-target binding interactions? 11. Drug A and B bind to the same biological target with the following binding constants: A; K eq = 1 x 10 5 M -1 B; K eq = 2.5 x 10 5 M -1 (a) Which compound binds more strongly to the target? (b) Calculate the difference in the free energy of binding (ΔΔG) between these two compounds. (c) Assuming that the target is present in the cell at low concentration, what fraction of the target biomolecule will be bound by A and B respectively? Drug concentrations = 1 x 10-6 M.

4 12. Inside cells, and in many bioassays, drugs must compete against endogenous ligands. The following relationship is often used to describe this competition: IC 50 = K D (1+[S]/K M ) Where IC 50 is the concentration of drug required to achieve 50% occupancy of the biological macromolecular target, K D is the dissociation constant for the drug-target complex, [S] is the concentration of the endogenous ligand, and K M is the dissociation constant for the endogenous ligandtarget complex. Assume that K D is 10 µm K M is 0.1 mm. Make a plot of IC 50 versus [S] across the range mm [S]. 13. Draw three amino acid side chains and indicate the possible types of "weak" bonding interactions that these functional groups can engage in with drug molecules. 14. What are the possible ways to discover lead compounds? What approach(es) is most widely used in modern drug discovery? 15. List three types of bioassay. Discuss the strengths and weaknesses of each. 16. The "rule of fives" was been developed as a guideline to describe "what a good drug should look like". Do your best to apply the "rule of five" to penicillin and valium (see structure in your text). Either try to calculate the Log P using the table that I gave you or use an online Log P calculator. Lipinski s rules were initially formulated from empirical observation (observations of facts without knowledge of the underlying reasons). onetheless, can you suggest chemical and medicinal principles underlying the "rule of fives"? 17. As discussed in your answer above, all things being equal, it is preferable to develop small compounds as potential drugs. This leads to the idea of ligand efficiency. (a) Write the equation that defines ligand efficiency. (b) calculate the ligand efficiency for the compound shown below (c) what is the empirically observed maximum value for ligand efficiency? H Cl H 2 K D = 125 nm MW =

5 18. Why did plants provide the first source of successful medicines? 19. At ph 8, how much of the lysine side chain will exist in the protonated, cationic form? (See acidbase calculations handout posted on the course website). 20. Draw the hydrogen bonding patterns for the backbone amide residues in an antiparallel beta sheet and an alpha helix. 21. In the most general terms, what do drug binding sites on proteins generally look like? 22. The protonation state of relevant functional groups is important in defining the types of noncovalent bonding interactions available to drugs and protein side chains. It is equally important to know where protonation occurs in drug molecules. This defines the true structure of the drug in physiological solution. (a) Predict the preferred site of protonation for the molecules shown below. Approach: protonate the molecules at each of the indicated sites. Then draw all of the possible good resonance structures for each protonation state. The ability to draw a larger number of high quality resonance structures is typically taken as a sign of stability. So, if you can draw more good resonance structures for a particular protonation state (site of protonation) protonation at this site is likely favored. Please see the review sheet on resonance structures on the following page. To calculate formal charges accurately it will help to always draw all lone pairs. H 2 H (b) The carboxylic acid side chain typically has a pk a of 5. Quickly estimate the percentage that exists in the deprotonated, anionic form at ph 7.

6 23. The van der Waals surface of a cationic group and an ionic group are 1.5 Å apart. How much does their interaction change (percent decrease or increase) if the ions are shifted so that they are 2.0 Å apart? 24. For the same two ions described above. When they are 1.5 Å apart how much does the strength of the attractive interacion differ in water versus dichloromethane (CH 2 Cl 2 ).

Introduction into Biochemistry. Dr. Mamoun Ahram Lecture 1

Introduction into Biochemistry Dr. Mamoun Ahram Lecture 1 Course information Recommended textbooks Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 7 th edition Instructors Dr. Mamoun