Chapter 13. Drug Design and Discovery

1. Chapter 13. Drug Design and Discovery

2. Drug Discovery Average time to bring a drug to market is 12-15 years. Average cost is $600-800 million. For every 20,000 compounds evaluated in animals, 10 make it to human clinical trials, of which 1 goes to market.

3. Clinical Trials Phase I (3-18 months) - evaluates safety, tolerability, pharmokinetics, and pharmacological effects in 20-100 healthy volunteers Phase II (1-3 years) - assesses effectiveness, determines side effects and other safety aspects, clarifies dosing in a few hundred patients Phase III (2-6 years) - establishes efficacy and adverse effects from long-term use with several thousand patients New Drug Application (NDA) submitted to FDA (4-36 months) Phase IV - results after drug is on market

4. Drug Discovery Drugs generally are not discovered directly; first a lead compound is identified. Lead compound Prototype having desired activity but also other undesirable characteristics, e.g., toxicity, other activities, insolubility, metabolism problems, oral bioavailability Lead modified by synthesis • to amplify desired activity • to minimize or eliminate undesirable properties Produces a drug candidate (compound worthy of extensive biological, pharmacological, and animal testing)

5. Drug Discovery Without a Lead Penicillins 1928 - Fleming Bacteria lysed by green mold; could not reproduce effect - serendipity. • mold spore contaminates culture dish • left dish on bench top while on vacation • weather was unseasonably cold • particular strain of mold was a good penicillin producer Could not get penicillin in a useful clinical form 1940 - Florey (Oxford) Succeeded in producing penicillin in a useful clinical form.

6. Structure of penicillin elucidated in 1944 - X-ray crystal structure by Dorothy Hodgkin (Oxford)

7. Lead Discovery First a bioassay (or screen) is needed Means to determine in vitro or in vivo, relative to a control, whether the compound has the desired activity* and relative potency**. * particular pharmacological effect (e.g., antibacterial effect) ** strength of the effect

8. High-throughput Screens (HTS) Very rapid, sensitive in vitro screens Can assay 100,000 compounds a day 1990 ~ 200,000 compounds screened per year 1995 ~ 5-6  106 compounds screened per year 2000 > 50  106 compounds screened per year in a large pharmaceutical company So far, no increase in rate of the number of drugs coming on the market.

9. Lead Discovery Approaches 1. Random screening - only approach before 1935; screen every compound you have; still a useful approach; streptomycin and tetracyclines identified in this way 2. Nonrandom (or Targeted or Focused) screening - only screen compounds related to active compounds 3. Drug metabolism studies - metabolites produced are screened for the same or other activities 4. Clinical observations - new activities found in clinical trials; Dramamine tested as antihistamine (allergy) - found to relieve motion sickness; Viagra tested as antihypertensive - found to treat erectile dysfunction

10. Lead Discovery Approaches (cont’d) 5. Rational approaches - identify causes for disease states: • imbalance of chemicals in the body • invasion of foreign organisms • aberrant cell growth Identify biological systems involved in disease states; use natural receptor ligand or enzyme substrate as the lead; a known drug also can be used as a lead

11. 13.1. 1. The biological targets of drug action

12. THE DRUG TARGET Human genome ~30,000 Druggable genome ~3000 Disease modifying genes ~3000 Drug targets ~600-1500 2-3x current #?

14. Schematic Model of NMDA receptor.

15. Rational Drug Design Chemical imbalances - antagonism or agonism of a receptor; enzyme inhibition Foreign organism and aberrant cell growth - enzyme inhibition; DNA interaction

16. Example of Rational Drug Design Serotonin (2.19), a mediator of inflammation, was used as the lead for the anti-inflammatory drug indomethacin (2.20).

17. Problems with Rational Approaches Cannot predict toxicity/side effects. Cannot predict transport/distribution. Cannot predict metabolic fate.

18. Lead Modification Pharmacodynamics receptor interactions - structure of lead is similar to that of the natural receptor ligand or enzyme substrate Pharmacokinetics ADME - absorption, distribution, metabolism, excretion; depends on water solubility and lipid solubility

19. Identification of the Active Part of the Lead First consider pharmacodynamics Pharmacophore - the relevant groups on the compound that interact with the receptor and produce activity Auxophore - the rest of the molecule

20. Structure-Activity Relationships (SARs) 1868 - Crum-Brown and Fraser Examined neuromuscular blocking effects of a variety of simple quaternary ammonium salts to determine if the quaternary amine in curare was the cause for its muscle paralytic properties. Conclusion: the physiological action is a function of chemical constitution

21. Structurally specific drugs (most drugs): Act at specific sites (receptor or enzyme) Activity/potency susceptible to small changes in structure Structurally nonspecific drugs: No specific site of action Similar activities with varied structures (various gaseous anesthetics, sedatives, antiseptics)

22. Example of SAR Lead: sulfanilamide (R = H) Thousands of analogs synthesized From clinical trials, various analogs shown to possess three different activities: • Antimicrobial • Diuretic • Antidiabetic

23. SARGeneral Structure of Antimicrobial Agents R = SO2NHR, SO3H • Groups must be para • Must be NH2 (or converted to NH2 in vivo) • Replacement of benzene ring or added substituents decreases or abolishes activity • R can be , , , • (but potency is reduced) • R = SO2NR2 gives inactive compounds

24. Structural Modifications Increase potency Increase therapeutic index - measure of the ratio of the concentration of a drug that gives undesirable effects to that which gives desirable effects e.g., LD50 (lethal dose for 50% of the test animals) ED50 (effective dose to give maximum effect in 50% of test animals) Therefore, want LD50 to be large and ED50 to be small. The larger the therapeutic index, the greater the margin of safety. The more life threatening the disease, the lower is an acceptable therapeutic index.

25. Types of Structural Modifications Homologation - increasing compounds by a constant unit (e.g., CH2) Effect of carbon chain length on drug potency Figure 2.3 Pharmacokinetic explanation: Increasing chain length increases lipophilicity and ability to cross membranes; if too high lipophilicity, it remains in the membrane Pharmacodynamic explanation: Hydrophobic pocket increases binding with increasing length; too large and does not fit into hydrophobic pocket

26. Branched chain groups are less lipophilic than straight chain groups. in throat lozenges

27. Often lowers potency and/or changes activity; interferes with receptor binding Chain Branching 10-Aminoalkylphenothiazines (X = H) R = CH2CHNMe2 promethazine antispasmodic/antihistamine activities predominate CH3 R = CH2CH2CH2NMe2 promazine greatly reduced antispasmodic/antihistamine activities greatly enhanced sedative/tranquilizing activities R = CH2CHCH2NMe2 trimepazine reduced tranquilizing activity enhanced antipruritic (anti-itch) activity All bind to different receptors CH3

28. Ring-Chain Transformations Transformation of alkyl substituents into cyclic analogs, which generally does not affect potency. Chlorpromazine (antipsychotic) (2.40, X = Cl, R = CH2CH2CH2NMe2) and (2.40, X = Cl, R = CH2CH2CH2N ) have equivalent tranquilizing effects

29. Trimepazine (2.40, X = H, R = ) and Methdilazine (2.40, X = H, R = ) have similar antipruritic (anti-itch) activities. Ring-chain transformation can have pharmacokinetic effects, such as increased lipophilicity or decreased metabolism.

30. Trimepazine (2.40, X = H, R = ) and Methdilazine (2.40, X = H, R = ) have similar antipruritic (anti-itch) activities. Ring-chain transformation can have pharmacokinetic effects, such as increased lipophilicity or decreased metabolism.

31. Bioisosterism Bioisosteres - substituents or groups with chemical or physical similarities that produce similar biological properties. Can attenuate toxicity, modify activity of lead, and/or alter pharmacokinetics of lead.

32. Classical Isosteres

33. Non-Classical Isosteres Table 2.3 Do not have the same number of atoms and do not fit steric and electronic rules of classical isosteres, but have similar biological activity.

35. Examples of Bioisosteric Analogues Table 2.4

36. Ionization has profound effect on lipophilicity (pharmacokinetics) and interaction with a receptor (pharmacodynamics). Neutral form crosses membranes, then re-establishes equilibrium with ionized form on other side. Ionized molecules that did not cross the membrane re-establish equilibrium with the neutral form, which can cross the membrane. At neutral pH there is a mixture of neutral and cationic forms.

37. The uricosuric drug phenylbutazone has a pKa of 4.5 and is active as an anion. Scheme 2.9 The pH of urine is ~ 4.8. Sulfinpyrazone has a pKa of 2.8 Therefore all in anionic form. 20 times more potent than phenylbutazone

38. In a cell-free system (no membranes), the antibacterial activity of sulfamethoxazole is directly proportional to the degree of ionization (pharmacodynamics). Scheme 2.10 In intact cells, where a drug must cross a membrane to get to the site of action, the antibacterial activity is proportional to its lipophilicity (neutral).