The Organic Chemistry of Drug Design and Drug Action

Chapter 3

Receptors

Receptors1878 Langley

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

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

Two fundamental characteristics of a receptor:

Recognition capacity - binding Amplification - initiation of response

Integral proteins embedded in phospholipid bilayer of membranes

Figure 2.26

Drug-Receptor InteractionsPharmacodynamics

Kd =[drug][receptor]

[drug-receptor complex] (3.1)

Driving force for drug-receptor interaction - low energy state of drug-receptor complex (binding energy)Kd - measure of affinity to receptor (a dissociation constant)

SCHEME 3.1 Equilibrium between a drug, a receptor, and a drug–receptor complex

Forces Involved in Drug-Receptor Complex

Molecular surfaces must be close and complementary

G° = -RTlnKeq (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)

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.

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.

Hydrogen BondingType 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.

Intramolecular hydrogen bonding

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

a-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.

-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.

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.

Charge-Transfer Complexes(molecular dipole-dipole interaction)

chlorothalonil-fungicide

acceptor donor

Figure 3.6G° ≈ -1 to -7 kcal/mol

FIGURE 3.6 Example of a charge-transfer interaction. Wavy line represents the receptor cavity.

Hydrophobic “Interactions”Increase in entropy of H2O 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.

Hydrophobic Interaction

butamben - topical anesthetic G° ≈ -0.7 kcal/mol per CH2/CH2 interaction

FIGURE 3.8 Example of hydrophobic interactions. The wavy line represents the receptor cavity.

π-π-Interactions

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

Cation-π-interactions

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

Halogen bonding

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

Van der Waals (London Dispersion) Forces

G° ≈ -0.5 kcal/mol per CH2/CH2 interaction

As molecules approach, temporary dipoles in one molecule induce opposite dipoles in another; therefore, producing an intermolecular attraction

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

Dose-Response Curve

Use any measure of response(LD50, ED50, etc.)

Means of measuring drug-receptor interactions

FIGURE 3.13 Effect of increasing the concentration of a neurotransmitter (ACh) on muscle contraction. The Kd is measured as the concentration of neurotransmitter that gives 50% of the maximal activity.

Full Agonist

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

Competitive Antagonist

Noncompetitive Antagonist

Different binding sites

Antagonists

X

NT + R NT R

X R

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).

Partial Agonistlow [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.

Inverse Agonistsfull 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′).

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

Agonists - often structural similarity

Antagonists - littlestructural similarity

Table 3.1

How can agonists and antagonists bind to same site and one show response, other not?

agonist antagonist enantiomer

• All naturally-occurring chemicals in the body are agonists• Most xenobiotics are antagonists• Drugs that bind to multiple receptors side effects

Two stages of drug-receptor interactions:

1) complexation with receptor 2) initiation of response

affinity efficacyintrinsic activity

(Stephenson)(Ariëns)

All are full agonists

5 different drugs = 1 full agonist < 1 partial 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.

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.

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

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.

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.

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?

Activation-Aggregation TheoryMonad, Wyman, Changeux (1965) Karlin (1967)

Receptor is always in a state of dynamic equilibrium between activated form (Ro) and inactive form (To).

Ro Tobiologicalresponse

no biologicalresponse

Agonists shift equilibrium to Ro

Antagonists shift equilibrium to To

Partial agonists bind to both Ro and To

Binding sites in Ro and To may be different, accounting for structural differences in agonists vs. antagonists

Two-state (Multi-state) Receptor ModelR 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.

Drug and Receptor ChiralityDrug-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

Topographical and Stereochemical ConsiderationsSpatial arrangement of atoms

Common structural feature of antihistamines (antagonists of H1 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

Chiral antihistamineKd 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

Distomer is really an impurity (“isomeric ballast”)

May contribute to side effects and/or toxicity

N

O

O

HNO O

H

N

O

O

HN OO

H

3.13

(R)-(+)-thalidomidesedative/hypnotic

(S)-(-)-thalidomideteratogen

Enantiomers of ketamine

S-ketamine is several fold more potent than R-ketamine

Prilocaine, a local anesthetic

Both enantiomers are active, but only one is toxic

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

Enantiomers can have different activities

S-enantiomer: NSAIDR-enantiomer: Reduces bone loss in periodontal disease

Enantiomers can have different activities

dextropropoxyphene (Darvon®)analgesic

levopropoxyphene (Novrad®)antitussive (anticough)

Enantiomers can have opposite activities

barbiturate

S-(+)-convulsive

R-(-)-narcotic

(actually inverse agonist)

One enantiomer may antagonize the other with no overall effect observed.

Enantiomers can have opposite activities

(+)-isomer: Narcotic agonist analgesic(-)-isomer: Narcotic antagonist

Enantiomers can have opposite activities

R-enantiomer: Serotonin agonist at 5HT-1aS-enantiomer: Serotonin antagonist at 5HT-1a

Stereospecificity of one compound can vary for different receptors

(+) - 3.24 butaclamol - antipsychotic(-) is almost inactive

Eudismic ratio (+/-) is 1250 for D2-dopaminergic, 160 for D1-dopaminergic, and 73 for -adrenergic receptors

Eudismic ratio (-/+) is 800

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

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

Epinephrine, a natural hybrid drug

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)

Omeprazole, a chiral switch

RS, Prilosec, now genericS-enantiomer, Nexium

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

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.

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

Verapamil is used as a racemate

S-enantiomer is an antihypertensiveR-enantiomer inhibits resistance of cancer cells

Receptor Interaction

Enantiomers cannot be distinguished with only two binding sites.

Figure 3.24

Three-point attachment concept

Figure 3.25

Receptor needs at least three points of interaction to distinguish enantiomers.

Unnatural enantiomers of natural products may have useful activities

Both of these are more active than the natural enantiomers!

Diastereomers

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

Diastereomers

The antipsychotic activity of 3.37a is 12 times more than 3.37b

Diastereomers

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

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

Figure 3.26

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

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 Kd 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).

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.

Consider acetylcholine binding to muscarinic and nicotine receptors

Me3NCH2CH2OCCH3

O

Me3NOAc

acetylcholine

Four conformers of acetylcholine (just staggered conformers)

Lowest energy conformer

Newman projections

Conformationally rigid analogs

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

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.

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)

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).

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.

Possible conformers of piperidino ring

F C

O

(CH2)3R =

Conformationally Rigid Analogs

order of potency3.51 > 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.

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.

Conformations of peptides

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

Atropisomers

FIGURE 3.29 General example of atropisomerization

What makes atropisomers stable?

FIGURE 3.30 Example of a nonatropisomer, an unstable atropisomer, and a stable atropisomer

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

Atropisomers in drug optimization

The active atropisomer of 3.58 is 3.59. 3.60 has two atropisomers3.61 has only a single isomer

A neurokinin 1antagonist is alead for an antidepressant

Avoiding atropisomers—make rotations fast

Symmetrization to avoid atropisomers

Ring Topology

chlorpromazine - tranquilizeramitriptyline - antidepressant with a tranquilizing side effect

imipramine - pure antidepressant

bending of ring planes torsional angleannellationangle of ring axes

tranquilizers - only mixed - and antidepressants - , ,

Figure 3.32

You must consider the 3-dimensional structures of rings.

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 H2 receptor

Nobel Prize (1988) to James Black for antagonist discovery

H1 and H2 receptors differentiated by agonist and antagonists

H1 receptor agonist (no effect on H2

receptor)

H2 - receptor agonist (no effect on H1 receptor)

H2 - receptor antagonists would be antiulcer drugs

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.

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

Isosteric replacement

Isothiourea 3.76 is more potent than the cyclic analogue 3.77

imidazole retained for recognition

not + charged

homolog

Had weak antagonistic activity without stimulatory activity.

Homologation

further homologation

R = CH3 burimamide

purely competitive antagonist for H2 receptor

Tested in humans - poor oral activity

Could be pharmacokinetics or pharmacodynamics

Consider pharmacodynamics

Imidazole ring can exist in 3 forms

FIGURE 3.33 Three principal forms of 5-substituted imidazoles at physiological pH

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

To increase potency of burimamide

Compare population of the imidazole form in burimamide at physiological pH to that in histamine.

Hammett Study of Electronic Effect of Side Chainfavored forR = e- -withdrawing

favored forR = e- -donating

pKa of imidazole = 6.80

pKa of imidazole in histamine = 5.90

Therefore, side chain is e- -withdrawing, favoring 3.80a.

pKa of imidazole in burimamide = 7.25

Therefore, side chain is e- -donating, favoring 3.80c.

Need to make side chain e- -withdrawing.

Isosteric replacement to lower the pKa 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 = CH3)

pKa of imidazole in metiamide = 6.80

8-9 times more potent than burimamide

thiaburimamide (R = H)

pKa of imidazole in thiaburimamide = 6.25

thiaburimamide is 3 times more potent than burimamide

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.

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.

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) (pKa -0.4)

X = N-NO2 (pKa -0.9)

Both are comparable to metiamide in potency but without the side effect.

FIGURE 3.35 Linear free energy relationship between H2 receptor antagonist activity (pA2) 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

A cyclic analogue is less active

Other H2 receptor antagonists made using cimetidine as the lead

ranitidine (Glaxo)

(no imidazole at all) famotidine (Yamanouchi)

nizatidine (Eli Lilly)

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

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

3.92 has low bioavailability and undergoes rapid metabolism

SCHEME 3.3 Oxidative metabolism of the 1,4-diazepane ring of 3.92

Further optimization

Methylation gave 3.95, which is resist to metabolism, but has low bioavailabilityFluorination and removal of a methyl group gave 3.96, which has better bioavailabilityAdding a benzoxazole in 3.97 reduces metabolism further, but has lower potencyAdding a chlorine increases potency, resulting in 3.98 (Suvorexant)

An alternative orexin antagonist

More potent than suvorexant in vivo