1. The Organic Chemistry of Drug Design and Drug Action Chapter 3 Receptors

2. 1878Langley Study of antagonistic action of alkaloids on cat salivary flow suggests the compounds interacted with some substance in the nerve endings

3. Receptors 1897 Ehrlich Side chain theory - Cells have side chains that contain groups that bind to toxins - termed receptors 1906 Langley Studying antagonistic effects of curare on nicotine stimulation of skeletal muscle Concluded receptive substance that received stimulus, and by transmitting it, caused muscle contraction

4. Two fundamental characteristics of a receptor:  Recognition capacity - binding  Amplification - initiation of response

5. Integral proteins embedded in phospholipid bilayer of membranes Figure 2.26

6. Drug-Receptor Interactions Pharmacodynamics (3.1) Driving force for drug-receptor interaction - low energy state of drug-receptor complex (binding energy) K d - measure of affinity to receptor (a dissociation constant) SCHEME 3.1 Equilibrium between a drug, a receptor, and a drug–receptor complex

7. Forces Involved in Drug-Receptor Complex Molecular surfaces must be close and complementary  G° = -RTlnK eq (3.2) Decrease in  G° of ~ 5.5 kcal/mol changes binding equilibrium from 1% in drug-receptor complex to 99% in drug-receptor complex Forces in drug-receptor complex generally weak and noncovalent (reversible)

8. Ionic Interaction Basic groups, e.g., His, Lys, Arg (cationic) Acidic groups, e.g., Asp, Glu (anionic) Figure 3.1  G° ≈ -5 kcal/mol FIGURE 3.1 Example of an electrostatic (ionic) interaction. Wavy line represents the receptor cavity.

9. Ion-Dipole and Dipole-Dipole Interactions Figure 3.2  G° ≈ -1 to -7 kcal/mol FIGURE 3.2 Examples of ion–dipole and dipole–dipole interactions. Wavy line represents the receptor cavity.

10. Hydrogen Bonding Type of dipole-dipole interaction between H on X-H (X is an electronegative atom) and N, O, or F Figure 3.3  G° ≈ -3 to -5 kcal/mol FIGURE 3.3 Examples of hydrogen bonds. Wavy line represents the receptor cavity.

11. Intramolecular hydrogen bonding FIGURE 3.4 Two examples (A and B) of how intramolecular hydrogen bonding can mimic a bioisosteric heterocycle.

12.  -helix 3.5 is an example of an α-helix in a protein—Copyright 2007 from Molecular Biology of the Cell, Fifth Edition by Alberts, et al. Reproduced by permission of Garland Science/Taylor & Francis LLC.

13.  -sheet 3.6 is an example of a β-sheet in a protein—Copyright 2007 from Molecular Biology of the Cell, Fifth Edition by Alberts, et al. Reproduced by permission of Garland Science/Taylor & Francis LLC.

14. DNA 3.7 is an example of a double helix in DNA—Copyright 2007 from Molecular Biology of the Cell, Fifth Edition by Alberts, et al. Reproduced by permission of Garland Science/Taylor & Francis LLC.

15. Charge-Transfer Complexes (molecular dipole-dipole interaction) chlorothalonil- fungicide acceptordonor Figure 3.6  G° ≈ -1 to -7 kcal/mol FIGURE 3.6 Example of a charge-transfer interaction. Wavy line represents the receptor cavity.

16. Hydrophobic “Interactions” Increase in entropy of H 2 O molecules decreases free energy. Therefore the complex is stabilized. FIGURE 3.7 Formation of hydrophobic interactions. From Korolkovas, A. (1970). Essentials of Molecular Pharmacology, p. 172. Wiley, New York. This material is reproduced with permission of John Wiley & Sons, Inc. and by permission of Kopple, K. D. 1966. Peptides and Amino Acids. Addison-Wesley, Reading, MA.

17. Hydrophobic Interaction butamben - topical anesthetic  G° ≈ -0.7 kcal/mol per CH 2 /CH 2 interaction FIGURE 3.8 Example of hydrophobic interactions. The wavy line represents the receptor cavity.

18. π-π-Interactions FIGURE 3.9 Example of π–π stacking. The wavy line represents the receptor cavity.

19. Cation-π-interactions FIGURE 3.10 Example of a cation–π interaction. The wavy line represents the receptor cavity.

20. Halogen bonding FIGURE 3.11 Example of halogen bonding. A compound bound into phosphodiesterase 5. The wavy line represents the enzyme cavity.

21. Van der Waals (London Dispersion) Forces  G° ≈ -0.5 kcal/mol per CH 2 /CH 2 interaction As molecules approach, temporary dipoles in one molecule induce opposite dipoles in another; therefore, producing an intermolecular attraction

22. Dibucaine - local anesthetic FIGURE 3.12 Example of potential multiple drug–receptor interactions. The van der Waals interactions are excluded.

23. Dose-Response Curve Use any measure of response (LD 50, ED 50, etc.) Means of measuring drug-receptor interactions FIGURE 3.13 Effect of increasing the concentration of a neurotransmitter (ACh) on muscle contraction. The K d is measured as the concentration of neurotransmitter that gives 50% of the maximal activity.

24. Full Agonist FIGURE 3.14 Dose–response curve for a full agonist (W).

25. Competitive Antagonist Noncompetitive Antagonist Different binding sites Antagonists FIGURE 3.15 (A) Dose-response curve for an antagonist (X); (B) effect of a competitive antagonist (X) on the response of a neurotransmitter (acetylcholine; ACh); (C) effect of varying concentration of a competitive antagonist X in the presence of a fixed, maximally effective concentration of agonist (ACh); and (D) effect of various concentrations of a noncompetitive antagonist (X’) on the response of the neurotransmitter (ACh).

26. Partial Agonist low [neurotransmitter] added agonist effect antagonist effect high [neurotransmitter] added FIGURE 3.16 (A) Dose–response curve for a partial agonist (Y); (B) effect of a low concentration of neurotransmitter on the response of a partial agonist (Y); and (C) effect of a high concentration of neurotransmitter on the response of a partial agonist (Y). In (C), the concentration of the neurotransmitter (a,b,c) is c > b > a.

27. Inverse Agonists full inverse agonist partial inverse agonist Addition of an agonist or antagonist to an inverse agonist (a, b, c are increasing concentrations of agonist added) FIGURE 3.17 (A) Dose–response curve for a full inverse agonist (Z); (B) effect of a competitive antagonist on the response of a full inverse agonist (a, b, and c represent increasing concentrations of the added antagonist or natural ligand to Z); and (C) dose–response curve for a partial inverse agonist (Z′).

28.  To effect a certain response of a receptor, design an agonist  To block a particular response of a natural ligand of a receptor, design an antagonist  To produce the opposite effect of the natural ligand, design an inverse agonist

29. Agonists - often structural similarity Antagonists - little structural similarity Table 3.1

30. How can agonists and antagonists bind to same site and one show response, other not? agonistantagonistenantiomer All naturally-occurring chemicals in the body are agonists Most xenobiotics are antagonists Drugs that bind to multiple receptors  side effects

31. Two stages of drug-receptor interactions: 1) complexation with receptor2) initiation of response affinity efficacy intrinsic activity (Stephenson) (Ariëns) All are full agonists 5 different drugs  = 1 full agonist  < 1partial agonists FIGURE 3.19 Theoretical dose–response curves illustrate (A) drugs with equal affinities and different efficacies (the top compound is a full agonist, and the others are partial agonists) and (B) drugs with equal efficacies (all full agonists) but different affinities.

32. Affinity and efficacy are uncoupled: a compound can have great affinity but poor efficacy (and vice versa). A compound can be an agonist for one receptor and an antagonist or inverse agonist for another receptor. A full or partial agonist displays positive efficacy. An antagonist displays zero efficacy. A full or partial inverse agonist displays negative efficacy.

33. Drug-Receptor Theories Occupancy Theory (1926) Intensity of pharmacological effect is directly proportional to number of receptors occupied Does not rationalize how two drugs can occupy the same receptor and act differently

34. Rate Theory (1961) Activation of receptors is proportional to the total number of encounters of a drug with its receptor per unit time. Does not rationalize why different types of compounds exhibit the characteristics they do.

35. Induced Fit Theory (1958) Agonist induces conformational change - response Antagonist does not induce conformational change - no response Partial agonist induces partial conformational change - partial response FIGURE 3.20 Schematic of the induced-fit theory. Koshland, Jr., D. E., and Neet, K. E., Annu. Rev. Biochem., Vol. 37, 1968. Annual Review of Biochemistry by Annual Reviews. Reproduced with permission of Annual Reviews via Copyright Clearance Center, 2013.

36. Macromolecular Perturbation Theory  Two types of conformational perturbation (Belleau)  Specific conformational perturbation allows molecule to induce a response  Nonspecific conformational perturbation does not result in a response  How to explain an inverse agonist?

37. Activation-Aggregation Theory Monad, Wyman, Changeux (1965)Karlin (1967) Receptor is always in a state of dynamic equilibrium between activated form (R o ) and inactive form (T o ). R o T o biological response no biological response Agonists shift equilibrium to R o Antagonists shift equilibrium to T o Partial agonists bind to both R o and T o Binding sites in R o and T o may be different, accounting for structural differences in agonists vs. antagonists

38. Two-state (Multi-state) Receptor Model R and R* are in equilibrium (equilibrium constant L), which defines the basal activity of the receptor. Full agonists bind only to R* Partial agonists bind preferentially to R* Full inverse agonists bind only to R Partial inverse agonists bind preferentially to R Antagonists have equal affinities for both R and R* (no effect on basal activity) In the multi-state model there is more than one R state to account for variable agonist and inverse agonist behavior for the same receptor type.

39. Drug and Receptor Chirality Drug-Receptor Complexes Receptors are chiral (all L-amino acids) Racemic mixture forms two diastereomeric complexes [Drug] R + [Drug] S + [Receptor] S [Drug] R [Receptor] S + [Drug] S [Receptor] S Have different energies and stabilities

40. Topographical and Stereochemical Considerations Spatial arrangement of atoms Common structural feature of antihistamines (antagonists of H 1 receptor) Pharmacophore - parts of the drug that interact with the receptor and cause a response Figure 3.22 CH-O, N-, CH-2 or 3 carbons

41. Chiral antihistamine K d for enantiomers are different - two diastereomers are formed (S)-(+)-isomer 200x more potent than (R)-(-)- More potent isomer - Less potent isomer - eutomer distomer Ratio of potencies of enantiomers - High eudismic ratio when antagonist has stereogenic center in pharmacophore eudismic ratio

42. Distomer is really an impurity (“isomeric ballast”) May contribute to side effects and/or toxicity 3.13 (R)-(+)-thalidomide sedative/hypnotic (S)-(-)-thalidomide teratogen

43. Enantiomers of ketamine S-ketamine is several fold more potent than R-ketamine

44. Prilocaine, a local anesthetic Both enantiomers are active, but only one is toxic

45. Drugs useful as mixtures of enantiomers Both are local anesthetics, But l-form is vasoconstrictor Diuretic, but one enantiomer causes uric acidretention, the other inhibits it

46. Enantiomers can have different activities S-enantiomer: NSAID R-enantiomer: Reduces bone loss in periodontal disease

47. Enantiomers can have different activities dextropropoxyphene (Darvon®) analgesic levopropoxyphene (Novrad ® ) antitussive (anticough)

48. Enantiomers can have opposite activities barbiturate S-(+)- convulsive R-(-)- narcotic (actually inverse agonist) One enantiomer may antagonize the other with no overall effect observed.

49. Enantiomers can have opposite activities (+)-isomer: Narcotic agonist analgesic (-)-isomer: Narcotic antagonist

50. Enantiomers can have opposite activities R-enantiomer: Serotonin agonist at 5HT-1a S-enantiomer: Serotonin antagonist at 5HT-1a

51. Stereospecificity of one compound can vary for different receptors (+) - 3.24 butaclamol - antipsychotic (-) is almost inactive Eudismic ratio (+/-) is 1250 for D 2 -dopaminergic, 160 for D 1 -dopaminergic, and 73 for  -adrenergic receptors Eudismic ratio (-/+) is 800

52. Hybrid drugs - different therapeutic activities propranolol (X = NH ) antihypertensive Antagonist of  -adrenergic receptor (  -blocker) - triggers vasodilation Eudismic ratio (-/+) is 100 But propanolol also is a local anesthetic for which eudismic ratio is 1

53. Pseudo-hybrid drug - multiple isomeric forms involved in biological activity labetalol - antihypertensive R,R- mostly  -blocker (eutomer for  -adrenergic block) S,R- mostly  -blocker (eutomer for  -adrenergic block) S,S- and R,S- almost inactive (isomeric ballast) FIGURE 3.23 Four stereoisomers of labetalol

54. Epinephrine, a natural hybrid drug

55. Racemates as Drugs  90% of  -blockers, antiepileptics, and oral anticoagulants on drug market are racemates  50% of antihistamines, anticholinergics, and local anesthetics on drug market are racemates  In general, 30% of drugs are sold as racemates Racemic switch - a drug that is already sold as a racemate is patented and sold as a single enantiomer (the eutomer)

56. Omeprazole, a chiral switch RS, Prilosec, now generic S-enantiomer, Nexium

57. Single enantiomer drugs are expected to have lower side effects Antiasthma drug albuterol binds to  2 -adrenergic receptors, leading to bronchodilation The (R)-(-)-isomer is solely responsible for effects; the (S)-(+)-isomer causes pulse rate increases, tremors, and decreased blood glucose and potassium levels

58. Sometimes, it is better to use the racemate than one isomer. In the case of the antihypertensive drug nebivolol, the (+)-isomer is a  -blocker; the (-)-isomer causes vasodilation by a different mechanism. Therefore, it is sold as a racemate to take advantage of both vasodilating pathways.

59. Prozac is the racemic drug. The R-enantiomer showed cardiotoxicity so the chiral switch failed

60. Verapamil is used as a racemate S-enantiomer is an antihypertensive R-enantiomer inhibits resistance of cancer cells

61. Receptor Interaction Enantiomers cannot be distinguished with only two binding sites. Figure 3.24

62. Three-point attachment concept Figure 3.25 Receptor needs at least three points of interaction to distinguish enantiomers.

63. Unnatural enantiomers of natural products may have useful activities Both of these are more active than the natural enantiomers!

64. Diastereomers The antihistamine activity of (E)-triprolidine (3.36a) is 1000-fold greater than the (Z)-isomer (3.36b).

65. Diastereomers  The antipsychotic activity of 3.37a is 12 times more than 3.37b

66. Diastereomers  Diethylstilbestrol (3.38a) is a much more potent estrogen than the Z-isomer (3.38b)

67. Conformational Isomers  Pharmacophore is defined by a particular conformation of a molecule (the bioactive conformation)  The conformer that binds need not be the lowest energy conformer  Binding energy can overcome the barrier to formation of a higher energy conformer

68. Figure 3.26 Note that the bioactive conformation bound to the peroxisome proliferator activated receptor gamma (PPAR  ) is not the lower energy extended conformation.

69. If the lead has low potency, it may be because of the low population of the active conformer. If the bioactive conformer is high in energy, the K d will appear high (poor affinity) because the population of the ideal conformer is low. SCHEME 3.2 Cyclohexane conformations. a, chair (substituent equatorial); b, half-chair; c, boat; d, half-chair; e, chair (substituent axial).

70. To determine the active conformation, make conformationally rigid analogs. The flexible lead molecule is locked into various conformations by adding bonds to rigidify it. First we will use this approach to identify the bioactive conformation of a neurotransmitter, then a lead molecule.

71. Consider acetylcholine binding to muscarinic and nicotine receptors acetylcholine

72. Four conformers of acetylcholine (just staggered conformers) Lowest energy conformer Newman projections

73. Conformationally rigid analogs All exhibited low muscarinic receptor activity, but 3.43a was most potent (0.06 times potency of ACh).

74. Analogues of acetylcholine  The threo isomer (3.44) is 14 time more potent than acetylcholine.  The erythro isomer (3.45) is 0.036 times as potent as acetylcholine.

75. To minimize the number of extra atoms, the cyclopropane analog was made. The (+)-trans isomer (3.46) has about the same muscarinic activity as acetylcholine; (-)-trans isomer 1/500th potency. Excellent support for the anti-conformer as the bioactive conformer. (  )-cis isomer (3.47) has negligible activity. Therefore, acetylcholine binds to the muscarinic receptor in an extended form (3.42a)

76. However, both the trans and cis cyclopropane analogs are weakly active with the nicotinic receptor for acetylcholine. Therefore, a conformation other than the anti- conformation must bind to that receptor (i.e., a higher energy conformer).

77. Conformationally Rigid Analogs in Drug Design moderate tranquilizing activity Maybe it is because the piperidino ring needs to be in a higher energy conformation for good binding.

78. Possible conformers of piperidino ring R =

79. Conformationally Rigid Analogs order of potency 3.51 > 3.52 > 3.50 Therefore, the less stable axial conformer binds better than the equatorial conformer. Lead modification should involve making analogs in which the hydroxyl group is preferred in an axial orientation.

80. Conformations of PCP FIGURE 3.27 PCP, 3.53 and three conformationally rigid analogs of PCP All these analogs bind poorly to the NMDA receptor, but bind well to the σ-receptor.

81. Conformations of peptides FIGURE 3.28 Use of a triazole as a conformationally rigid bioisostere to lock in an amide bond conformation

82. Atropisomers FIGURE 3.29 General example of atropisomerization

83. What makes atropisomers stable? FIGURE 3.30 Example of a nonatropisomer, an unstable atropisomer, and a stable atropisomer

84. Telenzepine racemizes very slowly FIGURE 3.31 Exceedingly slow isomerization of atropisomers of telenzepine (3.57) (+) isomer is 500 times more active at muscarinic acetylcholine receptors

85. Atropisomers in drug optimization The active atropisomer of 3.58 is 3.59. 3.60 has two atropisomers 3.61 has only a single isomer A neurokinin 1 antagonist is a lead for an antidepressant

86. Avoiding atropisomers—make rotations fast

87. Symmetrization to avoid atropisomers

88. Ring Topology chlorpromazine - tranquilizer amitriptyline - antidepressant with a tranquilizing side effect imipramine - pure antidepressant

89. bending of ring planes torsional angle annellation angle of ring axes tranquilizers - only  mixed -  and  antidepressants - , ,  Figure 3.32 You must consider the 3-dimensional structures of rings.

90. Case History of Rational Drug Design - Cimetidine (no QSAR, computer graphics, or X-ray crystallography) Another action of histamine - stimulation of gastric acid secretion Antihistamines have no effect on H 2 receptor Nobel Prize (1988) to James Black for antagonist discovery

91. H 1 and H 2 receptors differentiated by agonist and antagonists H 1 receptor agonist (no effect on H 2 receptor) H 2 - receptor agonist (no effect on H 1 receptor) H 2 - receptor antagonists would be antiulcer drugs

92. Bioassay used to screen compounds Histamine was infused into anesthetized rats to stimulate gastric acid secretion, then the pH of the perfusate from the stomach was measured before and after administration of the test compound.

93. Lead Discovery Histamine analogs synthesized at Smith, Kline, and French (now GlaxoSmithKline) Took four years and 200 compounds 3.75 was very weakly active (actually, partial agonist) N  -guanylhistamine

94. Isosteric replacement Isothiourea 3.76 is more potent than the cyclic analogue 3.77

95. imidazole retained for recognition not + charged homolog Had weak antagonistic activity without stimulatory activity.

96. Homologation further homologation R = CH 3 burimamide purely competitive antagonist for H 2 receptor Tested in humans - poor oral activity Could be pharmacokinetics or pharmacodynamics

97. Consider pharmacodynamics Imidazole ring can exist in 3 forms FIGURE 3.33 Three principal forms of 5-substituted imidazoles at physiological pH

98. Thioureido group can exist as 4 conformers Side chain can be in many conformations Maybe only a small fraction in the bioactive form FIGURE 3.34 Four conformers of the thioureido group

99. To increase potency of burimamide Compare population of the imidazole form in burimamide at physiological pH to that in histamine.

100. Hammett Study of Electronic Effect of Side Chain favored for R = e - -withdrawing favored for R = e - -donating pK a of imidazole = 6.80 pK a of imidazole in histamine = 5.90 Therefore, side chain is e - -withdrawing, favoring 3.80a. pK a of imidazole in burimamide = 7.25 Therefore, side chain is e - -donating, favoring 3.80c. Need to make side chain e - -withdrawing.

101. Isosteric replacement to lower the pK a of the imidazole A second way to increase population of 3.80a is to put an e - -donating group at 4-position. metiamide (3.82, R = CH 3 ) pK a of imidazole in metiamide = 6.80 8-9 times more potent than burimamide thiaburimamide (R = H) pK a of imidazole in thiaburimamide = 6.25 thiaburimamide is 3 times more potent than burimamide

102. Oxaburimamide is less potent than burimamide, even though O is more electronegative than S Conformationally-restricted analog forms by intramolecular H-bonding. Does not occur with thiaburimamide.

103. Metiamide (3.82)tested in 700 patients with duodenal ulcers - very effective. However, side effect in a few cases (granulocytopenia). Thought the side effect was caused by the thiourea group.

104. Isosteric replacement (X = O, X = NH) is 20 times less potent. When X = NH, basic To lower basicity, add e - -withdrawing group X = N-CN (cimetidine)(pK a -0.4) X = N-NO 2 (pK a -0.9) Both are comparable to metiamide in potency but without the side effect.

105. FIGURE 3.35 Linear free energy relationship between H 2 receptor antagonist activity (pA 2 ) and the partition coefficient. Reprinted with Permission of Elsevier. This article was published in Pharmacology of Histamine Receptors, Ganellin, C. R., and Parsons, M. E. (1982), p. 83, Wright-PSG, Bristol. Linear free energy relationship between potency and lipophilicity cimetidine

106. A cyclic analogue is less active

107. Other H 2 receptor antagonists made using cimetidine as the lead ranitidine (Glaxo) (no imidazole at all) famotidine (Yamanouchi) nizatidine (Eli Lilly)

108. Case history #2: Suvorexant Insomnia is a serious health problem Orexin A and B are neuropeptides that regulate sleep Orexins bind to a GPCR Orexin antagonists could be sleep aids

109. Merck identified a lead compound (3.89) from high throughput screening Modification of the aromatic rings gave 3.90, 3.91, and finally 3.92

110. 3.92 has low bioavailability and undergoes rapid metabolism SCHEME 3.3 Oxidative metabolism of the 1,4-diazepane ring of 3.92

111. Further optimization Methylation gave 3.95, which is resist to metabolism, but has low bioavailability Fluorination and removal of a methyl group gave 3.96, which has better bioavailability Adding a benzoxazole in 3.97 reduces metabolism further, but has lower potency Adding a chlorine increases potency, resulting in 3.98 (Suvorexant)

112. An alternative orexin antagonist More potent than suvorexant in vivo