An Introduction to. Medicinal Chemistry

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1 An Introduction to Medicinal Chemistry GRAHAM

2 Oxford University Press, Walton Street, Oxford OX2 6DP Oxford

3 Preface This text is aimed at undergraduates who have a basic grounding in chemistry and are interested in a future career in the pharmaceutical industry. It attempts to convey something

4 Acknowledgements Figure

5 Contents Classification of drugs xiii 1. Drugs

6 viii Contents

7 Contents

8 x Contents 10.5 Antibacterial agents which inhibit cell wall synthesis Penicillins Cephalosporins

9 Contents xi Structure

10 xii Contents Conformational isomers Desolvation Variation

11 Classification of drugs

12 xiv Classification

13 1 Drugs and the medicinal chemist In medicinal chemistry, the chemist attempts to design and synthesize a medicine or a pharmaceutical agent which will benefit humanity. Such

14 Drugs

15 Whilst penicillin Drugs and the medicinal chemist 3

16 4 Drugs and the medicinal chemist The drug is called diamorphine and it is the drug of choice when treating patients dying

17 Drugs

18

19 Drugs

20

21

22 10 The why and the wherefore Cytoplasm Nucleus Nuclear membrane Cell membrane Fig. 2.1 A typical cell. Taken from J. Mann, Murder, magic, and medicine, Oxford University Press (1992), with permission. Polar Head Group Polar Head Group Hydrophobia Tails Hydrophobia Tails Fig.

23 Where

24 12

25 Where do drugs work? 13 Amphotericin is a fascinating molecule in that one half of the structure is made up of double bonds and is hydrophobic, while the other half contains a series of hydroxyl groups

26 14

27 3 Protein structure In order to understand how drugs interact with proteins, it is necessary to understand their structure. Proteins have four levels of structure primary, secondary, tertiary, and quaternary. 3.1 The primary structure of proteins

28 16 Protein structure [ H O

29

30 18 Protein structure H R 0 H ^ ^ ^ H-bonds O R H O Antiparallel Chains Residues / above,x

31 The tertiary structure of proteins 19 CD2 H24 Fig.

32 20 Protein structure I I I 10 \\

33 The tertiary structure of proteins Covalent bonds Covalent bonds

34 22 Protein structure Fig Hydrogen bond Van der Waals bonds Bond strength

35

36 24 Protein structure H-Bond Peptidef Chain r Peptide Chain Fig Bonding interactions with water. Therefore,

37 The quaternary structure of proteins 25 number of ionic and hydrogen bonds contributing to the tertiary structure is reduced.

38 26 Protein structure again that tertiary structure

39

40 28 Drug action at enzymes Energy Transition State New Transition State Product WITHOUT CATALYST WITH CATALYST Product Fig. 4.2 Activation energy. Energy difference

41

42

43 Substrate binding

44 32 Drug action at enzymes Fig.

45 Substrate binding at an active site 33 unable to accept any more substrate. Therefore, the bonding interactions between substrate and enzyme have to be properly balanced such that they are strong enough to keep

46 34 Drug action

47 Substrate binding

48

49 The catalytic role of enzymes 37 Fig Mercaptopurine. an example of an allosteric inhibitor. It inhibits the first enzyme involved in the synthesis of purines and therefore blocks purine synthesis. This in turn blocks DNA synthesis. 4.5 The catalytic role of enzymes We

50

51

52

53 The catalytic role of enzymes 41 R Thymidylate Synthetase HN X o R

54 42 Drug action

55 The catalytic role I NH 2 CHO (OH Condensation R<

56 44 Drug action at enzymes met in the body and would have shown little or no selectivity. (The uses of alkylating agents

57 5

58

59 Nerve Neurotransmitters

60 48 Drug action at receptors CH 2 + xnme3 NHR Acetylcholine R=H Noradrenaline R=Me Adrenaline NH Dopamine Serotonin H 2NL CH 2 k CH 2 5-Hydroxytryptamine Fig. Gamma-aminobutanoic acid

61 Receptors

62 50 Drug action at receptors Fig. 5.5 Binding of a messenger to a receptor. reaction takes place, what

63

64 52 Drug action at receptors Induced Fit and Opening

65 How does the message get received? 53 Receptor Enzyme Active site (open) Receptor Enzyme CD MESSENGER LJ Receptor im Enzyme X MESSENGER Receptor Enzyme Fig.

66 54 Drug action at receptors MESSENGER MESSENGER Receptor v^/ Enzyme No Reaction Fig Membrane-bound enzyme deactivation. change in shape conceals the active site, shutting down that particular reaction (Fig. 5.10). Neurotransmitters switch

67 process whereby How does a receptor change shape? 55

68 56 Drug action at receptors RECEPTOR PROTEIN CYTOPLASM Fig Receptor protein positioned

69

70 58 Drug action at receptors neurotransmitter. The binding forces must be strong enough to bind the neurotransmitter effectively such that the receptor changes shape. However, the binding forces cannot be too strong, or else the neurotransmitter would not be able to leave and the receptor would not be able to return to its original shape. Therefore, it is reasonable to assume that

71

72 60 Drug action at receptors left-handed ammo acids) are also present as single enantiomers and therefore catalyse enantiospecific reactions reactions which give only

73 A thorough understanding The design of antagonists 61

74 62 Drug action

75 Partial agonists 63 RECEPTOR RECEPTOR Fig Antagonism

76 64 Drug action

77 Tolerance and dependence Desensitization Some drugs bind relatively strongly

78 66 Drug action at receptors D Neurotransmitter Receptor Synthesis \ u \ I// u. D Increase Antagonist D Fig Process of increasing cell sensitivity. for what little neurotransmitter

79 Tolerance and dependence 67 level. During this period, the patient may be tempted to take the drug again in order to 'return

80

81 Structure of DNA 69 NH 2 NHo NHo Adenine Guanine. ^Cytosine H Thymi Purines Fig. Pyrimidines

82 70 Nucleic acids 6.1.2

83 Structure

84 72 Nucleic acids able to coil into a 3D shape and this is known as super-coiling. During replication, the double strand of DNA must unravel, but due to the tertiary supercoiling this leads to a high level

85 Drugs acting

86 74 Nucleic acids Fig. 6.9 Proflavine. best agents

87 Drugs acting on DNA 75 CH3 N: MECHLORETHAMINE

88

89 Ribonucleic acid

90 78 Nucleic acids end AMINO «A/* Base Pairing ml Methylmosine I Ino.ic UH 2 Dihydraundine

91 Ribonucleic acid 79 GROWING PROTEIN Growing Protein Fig Protein synthesis. Messenger

92

93 Summary 81

94

95 the never-ending quest Structure determination 83

96 84 Drug development

97 Structure-activity relationships

98 86 Drug development Potential Ionic Binding Sites O Potential

99 Structure-activity relationships

100 88 Drug development bonding or not, it could be replaced with an isosteric group such as methyl (see later). This would be more conclusive, but synthesis is more difficult. Another possibility

101 Synthetic analogues

102 90 Drug development Variation

103 Synthetic analogues

104 92 Drug development covered

105 Synthetic analogues

106 94 Drug development avoiding patent restrictions

107 Synthetic analogues

108 96 Drug development,oh OH GLIPINE A Fig Glipine analogues. B Me- COCAINE H Et 2NCH 2CH 2 O C O PROCAINE Fig Cocaine

109 Receptor theories 97 NH 2 Me BOND ROTATION RECEPTOR 1 RECEPTOR

110

111 Receptor theories

112

113

114 102 Drug development Frequently,

115 Lead compounds

116 104 Drug development O IIS NH C NH-CH2CH2CH2CH3 O O Fig Cimetidine. Fig Tolbutamide. described above. Clearly, this is a more demanding objective, but the cimetidine story proves that

117 A case study oxamniquine

118 Et 2NCH 2CH 2 CH 2NEt 2

119 A case study oxamniquine

120 108 Drug development Zero Activity Fig Addition of a methyl group. _ Net [ CH 2- CH 2-NH 2R

121 A case study oxamniquine 109 CH 3 Cl Fig Structure V. CH 2 OH Fig Oxamniquine. Adding

122 110 Drug development found

123

124 112 Pharmacodynamics stream. Thirdly,

125 Drug distribution and 'survival' 113 OXIDATIONS (catalysed by cytochrome P-450) Oxidation

126

127 Drug dose levels 115 can easily negotiate the fatty cell membranes get mopped up by fat tissue or are too weak to bind to their receptor sites. Consequently,

128 116 Pharmacodynamics Drugs

129 Drug design for pharmacokinetic problems 117 NH C CH 2CH2NEt 2 LIDOCAINE A further example of these tactics is provided in the penicillin field with methicillin (Chapter 10) Metabolic blockers Some drugs

130 118 Pharmacodynamics Other common metabolic reactions include aliphatic and aromatic C-hydroxylations (Fig. 8.7), N- and S-oxidations, O- and S-dealkylations, and deamination. Susceptible groups

131 Drug design

132 120 Pharmacodynamics

133 Drug design for pharmacokinetic problems 121 Blood Suppy Brain Cells H2N^ COOH COOH L-Dopa ^N Enzyme Dopamine Fig Transport

134 122 Pharmacodynamics Me AZATHIOPRINE 6-MERCAPTOPURINE Fig Azathioprine acts

135 Drug design for pharmacokinetic problems 123 Fig SALICYLIC ACID ASPIRIN R = H

136 124 Pharmacodynamics Many peptides

137 Drug design for pharmacokinetic problems 125 C O CH 2CH 2NEt 2 O ADRENALINE PROCAINE Fig used successfully in this respect and effectively inhibits dopa decarboxylase. Furthermore, since it is a highly polar compound containing two phenolic groups, a hydrazine moiety,

138 126 Pharmacodynamics Self-destruct drugs Occasionally, the problems faced are completely the opposite of those mentioned above.

139 grown Neurotransmitters as drugs? 127

140

141 Graphs and equations 129 What are these physicochemical features which we have mentioned? Essentially, they refer

142 130 Quantitative structure-activity relationships (QSAR) Log(l/C) Fig.

143 Physicochemical properties

144 132 Quantitative structure-activity relationships (QSAR)

145 Physicochemical properties

146 134 Quantitative structure-activity relationships (QSAR) words, compounds having

147 Physicochemical properties

148 136 Quantitative structure-activity relationships (QSAR) fact true constants and are accurate only for the structures from which they were derived. They

149 Physicochemical properties

150 138 Quantitative structure-activity relationships (QSAR) Benzole acids containing electron donating substituents will have smaller K x values than benzoic acid itself and hence the value of a

151 Meta Hydroxyl Group Physicochemical properties 139

152 140 Quantitative structure-activity relationships (QSAR) O P OEt Fig Diethyl phenyl phosphate. # Q Et membrane

153 Quantifying steric properties Hansch equation 141

154 142 Quantitative structure-activity relationships (QSAR) activity is related to only one such property, a simple equation can be drawn up. However, the biological activity of most drugs is related to a combination of physicochemical properties. In such cases, simple equations involving only one parameter are relevant only if the other parameters are kept constant. In reality, this is not easy to achieve and equations which relate biological activity to more than one parameter are more common. These equations are known as Hansch equations and they usually relate biological activity

155 log [I] The Craig plot 143

156 144 Quantitative structure-activity relationships (QSAR) + CT 1.0 NO 2 SOjNHj CH3SO2 3. CONH 2 CN * CH 3CO '- 4 CH 3CONH COjH CF 3 C? Br OCF T 7C OH OCH t-butyl NMej CT Fig Craig plot. 9.16

157 The Topliss scheme 145 and electron withdrawing properties (positive IT and positive a), whereas an OH substituent

158 146 Quantitative structure-activity relationships (QSAR) H, CH 2OCH 3 CH 3. Pr«E

159 The Topliss scheme 147 with a negative a factor (i.e. 4-OMe). If activity improves, further changes are suggested to test

160 148 Quantitative structure-activity relationships (QSAR) Order of Synthesis R Biological Activity High Potency A AA N N\k CH2CH2CO2H H 4-C1 4-MeO 3-C1 3-CF 3 3-Br 3-1 3,5-Cl 2 _ L LM L M L M * * * M= More Activity L= Less Activity

161 Planning

162 150 Quantitative structure-activity relationships (QSAR) activity. For example, a hydrophobia substituent may be favoured in one part of the skeleton, while

163 Case study

164 152 Quantitative structure-activity relationships (QSAR) group

165

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