The Organic Chemistry of Drug Design and Drug Action

Chapter 1

Introduction

Drug DiscoveryOne way to “discover” drugs

Figure 1.1

Medicinal Chemistry

The science that deals with the discovery or design of new therapeutic agents and their development into useful medicines.

It involves:

• Synthesis

• Structure-Activity Relationships (SAR)

• Receptor interactions

• Absorption, distribution, metabolism, and excretion (ADME) and toxicology

Medicinal Chemistry FolkloreEarliest medicines ~ 5100 years ago

Chinese emperor Shen Nung - book of herbs, Pen Ts’ao

Modern therapeutics:

Extract of foxglove plant, cited by Welsh physicians in 1250. Used to treat dropsy (congestive heart failure) in 1785 Contains digitoxin and digoxin; today called digitalis

Ma Huang Used as a heart stimulant and for nasal and chest congestion.

Contains ephedrine

Drugs from traditional sources

Quinine came from South America

Digitalis came from foxglove in Britain

Discovery of New DrugsNature is still an excellent source of new drugs (or precursors of new drugs).

Almost 40% of new drugs approved in the last 20 years are natural products or derived from natural products.

60% of antitumor and anti-infective drugs are natural products or derived from natural products.

Drug Discovery Without a LeadPenicillins1928 - Fleming

• 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

Discovery was not published until late 1940’s after World War II so Germans would not benefit from it.

Bacteria lysed by green mold; could not reproduce effect - serendipity.

Could not get penicillin in a useful clinical form

1940 - Florey (Oxford)Succeeded in producing penicillin in a useful clinical form.

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

Sulfa antibiotics were discovered in 1935

Serendipitous Discovery of Librium without a Lead

In 1955 Roche set out to prepare a series of benzheptoxdiazines (1.14) as potential new tranquilizer drugs, but the actual structure was found to be that of a quinazoline 3-oxide (1.15).

No active compounds were found, so the project was abandoned

In 1957, during a lab cleanup, a vial containing what was thought to be 1.16 was sent for testing, and it was highly active.

Further analysis showed that the actual structure of the compound was the benzodiazepine 4-oxide, 1.13, presumably produced in an unexpected reaction of the corresponding chloromethyl quinazoline 3-oxide (1.16) with methylamine.

Scheme 1.1

Librium

Valium is a more active analogue of Librium

Drugs from Drug Metabolism Studies

The nonsedating antihistamine terfenadine (Seldane) caused abnormal heart arrhythmias in some patients (binds to hERG*), so it was withdrawn from medical use.

*human Ether-a-go-go Related Gene

Fexofenadine (Allegra), a metabolite ofterfenadine, also is a nonsedatingantihistamine that does not cause heartarrhythmias, so it replaced terfenadine

Sulindac is metabolized to the active compound

(prodrug)

Drug Discovery from Clinical Observations

Viagra (sildenafil citrate) tested as antihypertensive/ antianginal drug.

Phase II trials not great, so went back to Phase I (healthy volunteers) at a higher dose.

Very happy volunteers .Reported prolongation of penile erections

increasedblood flow

decreasedblood flow

smoothmuscle relaxation

smoothmuscle constriction

Phosphodiesteraseisozyme in corpus cavernosum (in penis)

NO

Guanylate cyclase

Nitric oxide

cGMPGTP

L-Arg

stimulatessynthase

Erection

Mechanism of Action of Viagra

PDE 5

GMP

increasedblood flow

decreasedblood flow

NO

Guanylate cyclase

Nitric oxide

cGMPGTP

L-Arg

stimulatessynthase

smoothmuscle relaxation

Erection

Mechanism of Action of Viagra

Viagra blocksthis enzyme

Phosphodiesteraseisozyme in corpus cavernosum (in penis)

PDE 5

smoothmuscle constriction

GMP

Dramamine and Zyban also were found from side effects in clinical trials

Rational Drug DiscoveryDrugs generally are not discovered directly; first a lead compound is identified.Lead compoundPrototype having desired activity but also other undesirable characteristics, e.g., toxicity, other activities, insolubility, metabolism problems, oral bioavailabilityLead modified by synthesis

Produces a drug candidate (compound worthy of extensive biological, pharmacological, and animal testing)

• to amplify desired activity• to minimize or eliminate undesirable properties

Drug Discovery

Average time to bring a drug to market is 12-15 years.

For every 20,000 compounds evaluated in animals, 10 make it to human clinical trials, of which 1 goes to market.

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

Lead Discovery Approaches1. 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

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

Rational Drug Design

Identify Target

Chemical imbalances - antagonism or agonism of a receptor; enzyme inhibition

Foreign organism and aberrant cell growth - enzyme inhibition; DNA interaction

Protein drug targets

Examples of drug target-dopamine D3 receptor

FIGURE 1.4 Small molecule drug (quinpirol) bound to its protein target (dopamine D3 receptor). The cartoon on the right shows how a protein, such as the D3 receptor, spans the membrane of a cell. The D3 receptor in red depicts its conformation when the drug is bound. The D3 receptor in yellow depicts its conformation when no drug is bound. “TM” designates a transmembrane domain of the protein. Note the significant differences between the red and yellow regions on the intracellular side of the membrane, prompted by the binding of quinpirol from the extracellular side (Ligia Westrich, et al. Biochem. Pharmacol. 2010, 79, 897–907.) On the right is a molecular representation of the fluid mosaic model of a biomembrane structure. From Singer, S. J.; Nicolson, G L. Science. 1972, 175, 720. Reprinted with permission from AAAS.

Example of drug target-DNA

FIGURE 1.5 Small molecule drug (daunomycin) bound to its nucleic acid target (DNA). The different colors represent C (yellow), G (green), A (red), and T (blue). Mukherjee, A.; Lavery, R.; Bagchi, B.; Hynes, J. T. On the molecular mechanism of drug intercalation into DNA: A computer simulation study of the intercalation pathway, free energy, and DNA structural changes. J. Am. Chem Soc. 2008, 130, 9747. Reprinted with permission from Dr. Biman Bagchi, Indian Institute of Science, Bangalore, India. Journal of the American Chemical Society by American Chemical Society. Reproduced with permission of American Chemical Society in the format republish in a book via Copyright Clearance Center.

Example of drug target-enzyme

FIGURE 1.6 Interaction of the drug zanamivir with its enzyme target neuraminidase. (a) Model derived from an X-ray crystal structure; zanamivir is depicted as a space-filling model at center: carbon (white), oxygen (red), nitrogen (blue), and hydrogen (not shown). Only the regions of the enzyme that are close to the inhibitor are shown: small ball and stick models show key enzyme side chains (b) Schematic two-dimensional representation showing noncovalent interactions (dotted-lines) between zanamivir and the enzyme.

The biosynthesis of cholesterol is a target for

statin drugs

Acetylcholinesterase is a target for Alzheimer’s drugs

Problems with Targeted Approaches

• Cannot predict toxicity/side effects.

• Cannot predict transport/distribution.

• Cannot predict metabolic fate.

• Target in vivo may not be the desired one.

Drugs with unexpected targets

• Ezetimibe--designed to inhibit cholesterol esterase, but inhibits cholesterol transport

• Pregabalin—designed to activate Glu decarboxylase, but blocks Ca2+ channels

Alternatives to targets for lead discovery

• Natural substrate or ligand—modify the structure to obtain desired property.

• Natural product—can be adapted to bind to enzyme or receptor

• Screening—screen large number of compounds to find those that have the desired property

Drug based on a natural ligand

Drug based on natural products

High-throughput Screens (HTS)Very rapid, sensitive in vitro screens

Carried out robotically in 1536- or 3456-well titer plates on sub-microgram amounts of compound

Can assay 100,000 compounds a day

1990 ~ 200,000 compounds screened per year1995 ~ 5-6 106 compounds screened per year2000 > 50 106 compounds screened per year in a large pharmaceutical company

Increase in number of hits (compounds that elicit a predetermined level of activity)

So far, no increase in rate of the number of drugs coming on the market.

Other Screening ApproachesPossible to screen compounds for inhibition of an entire metabolic pathway:

• Combine all enzymes in the pathway (e.g., bacterial cell wall biosynthesis), add compound, look for accumulation of an intermediate in the pathway (inhibition of the enzyme that acted on the intermediate).

Screening also done by electrospray ionization mass spectrometry.

• Can add large number of compounds (as long as they have different molecular masses) and look for formation of noncovalent drug-receptor complexes in the mass spectrum. The affinity of the ligand (a small molecule that binds to a receptor) is measured by increasing the collision energy of the spectrometer.

Lead Modification

Pharmacodynamics Potency of drug binding to the target.

Pharmacokinetics ADME - Absorption, Distribution, Metabolism, Excretion; depends on water solubility and lipid solubility

Toxicity Often due to binding of the drug to unwanted off-targets—e.g., other enzymes or receptors.

Toxicity from off-target effects

Clinical TrialsPhase I (3-18 months) - evaluates safety, tolerability, pharmacokinetics, 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

Epilogue• For every 20,000 compounds tested in animals, 10 go to

clinical trials, and 1 goes to market

• 12-15 years of research (constant since 1980)

• Cost to get to market

1962 - $4 million

1996 - $350 million

2002 - $600-$800 million

2013 - $1.2-1.8 billion

• Only ~6000 known drugs of the estimated 1060 possible compounds

Epilogue (cont’d)

• Only ~400-500 different human targets known (< 1% of human proteome) - may be 5,000-10,000 potential drug targets

• Genomics (identification of new gene targets) and proteomics (identification of proteins expressed) are new directions for drug discovery

• In 2002, for the first time in U.S., generic drug sales were greater than nongeneric drug sales

• In 2002, only 16 new drugs entered the market (usually 20s or 30s)

• In 2013, 27 new drugs were approved

Number of New Drugs Declines as R&D Spending Increases

Taken from the Wall Street Journal, February 24, 2004

53

1621

Year ‘04New Drugs 36

‘05 20

‘06 22

‘07 17

‘08 24

‘09 25

‘10 21

‘11 35

‘12 39

‘13 27

‘14 41