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Abt. Simulation biologischer Systeme WSI/ZBIT, Eberhard-Karls-Universität Tübingen Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET
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Page 1: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Abt. Simulation biologischer Systeme WSI/ZBIT, Eberhard-Karls-Universität Tübingen

Drug Design 2

Oliver Kohlbacher Winter 2009/2010

12. ADMET

Page 2: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Overview

•  ADME –  Bioavailability

–  Metabolization, Elimination

•  Toxicity –  Effect and side effects

–  Mechanisms of toxicity

–  Models •  Animal models

•  In vitro models

•  Theoretical models and predictions

Page 3: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Failure in Late Development

•  90% of all drug candidates

fail between discovery and

introduction to the market

•  The late development phases

are the most expensive

phases

•  In more than 60% of the

cases, poor pharmacokinetic

(PK) or toxicological properties are the cause

Prentis et al., Br. J. Clin. Pharmacol. 1988, 25, 387-396.

6%

22%

41%

31%

Reason for Failure

Market Toxicity PK Efficacy

Page 4: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Absorption and Elimination

Central Compartment Biliary Renal

Gehirn

Blood-Brain Barrier

Enteral

Absorption

Elimination

Membranes of the GI Tract

Page 5: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Overview of the Different Areas

Application

Dissolution

Absorption

Distribution

Place of Action (Receptors)

Pharmacological Effect

Clinical Effect Toxic Effect

Storage

Biotransformation

Excretion

After: Mut, p. 5

Pharmaceutical Phase

Pharmacokinetic Phase

Pharmacodynamic Phase

Page 6: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Bioavailability

•  Drug has to reach the place of action and achieve a sufficient concentration there for the duration of action

•  This bioavailability is a key criterion for the effectiveness of a drug

•  Also summarized as ADME (Absorption, Distribution, Metabolism, Excretion) and ADMET (ADME-Tox)

–  Pharmaceutical basics: see Lecture Drug Design 1

–  Absorption and Distribution are pharmacokinetic properties

–  Metabolization is much harder to predict

–  It is not only relevant for the prediction of elimination, but also for toxicity (toxic metabolites!)

Page 7: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

First Pass Effect

Gastro-intestinal lumen

Gastro-intestinal wall

Liver Blood vessel

Biotransformation Elimination, Biotransformation

•  Absorbed substances have to pass through the gastro-intestinal wall then then through the liver (portal vein)

•  First pass effect: metabolization in the liver before the compound reaches systemic circulation, reduces bioavailability drastically

Page 8: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Biotransformation

•  Oxidation •  Reduction •  Hydrolysis •  Decarboxylation •  Methylation •  Acetylation

•  Conjugation with –  Activated glucuronic

acid –  Sulfuric acid –  Glycine

•  ...

•  Many enzymes catalyze the transformation of substrate families that also include numerous drugs

•  Particularly active in this regard are liver enzymes, which also happen to have a broad substrate specificity

•  Frequent biotransformations are:

Page 9: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Bioavailability

•  Experimental determination of ADME

parameters is time-consuming and costly

•  Computational could thus have a large impact

•  Bioavailability is not governed by a single

property, it is the sum of all ADME processes

•  Modeling it is thus very difficult and QSPR

models still have limited reliability in this

area

Page 10: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Models in Use System Models Pros Cons

In silico (Q)SAR, (Q)SPR

High throughput, cheap, easy to use

Require high-quality exp. data, not all biological processes modeled

In vitro Artificial membranes, cell-based assays (Caco2, MDCK)

Medium to high throughput, includes active and passive transport mechanisms

Many phenomena are strongly model-dependent, no active transport (membrane-based), analytically difficult

In situ Rat intestinal perfusion

Very close to in vivo, includes all key mechanisms except for systemic effects

Labour-intensive, differences between species In vivo Rat portal vein

studies As in situ but also includes presystemic metabolism

Pelkonen et al.; Eur J Clin Pharmacol 57:621-629, 2001

Page 11: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Experimental Models in vitro

in situ

in vivo

http://www.transonic.com http://www.uv.es/~mbermejo/projects.htm

http://www.millipore.com

Page 12: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

QSPR Model

•  Turner et al. published a purely computational study for bioavailability in 2003

•  169 with literature data on bioavailability

•  10 cpds. Randomly selected as a test set

•  Training on the remaining 159

•  Model based on eight different descriptors

•  Selected from 94 descriptors by stepwise multiple linear regression

•  Prediction: R = 0.72 Turner et al.; Anal Chim Acta 485;89-102, 2003

Page 13: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

QSPR Model

• Descriptors used: –  Electron affinity (H-bonds) –  Number of aromatic rings –  Energy of the highest occupied molecular

orbital (HOMO energy) –  Partition coefficient octanol/water (log P) –  Molar volume –  Ratio of hydrophilic/lipophilic groups –  Solubility in water –  Contribution of H-bonds to solubility

Turner et al., Anal Chim Acta (2003), 485, 89-102

Page 14: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Prediction of Bioavailability

Turner et al., Anal Chim Acta (2003), 485, 89-102

Page 15: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Toxicity and Side Effects

•  Are there drugs without side effects? • W. Kuschinski:

“If it is claimed that a substance has no side effects, then it is to be assumed that it has no desired effect either.“

•  Required: Estimate of toxicity

Page 16: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Toxicity and Side Effects

•  Paracelsus: „The dose makes the poison“

•  No clear distinction between ‘medicine’ and

‘poison’

•  Usually, there is not a single ‘cause’ for a

toxic effect

•  Many mechanisms are involved

•  Toxic effect often also occurs through

metabolization of the substance

Page 17: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Dose-Response Relationships

•  „The dose makes the poison“ –  Typically, an increase in dose

increases the effect –  Above a certain dose, additional

toxic effects may be observed –  Strength/duration of effect depends

on many factors, e.g., genotype, age, body mass, …

–  Difficult to quantify strength of the response

) Dose-response relationships

measured for collectives –  ED50: median effective dose –  LD50: median lethal dose

Katzung, Basisc and Clinical Pharmacology, p. 30

Page 18: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Therapeutic Index

Mut, S. 81

ED50 LD50

•  Therapeutic index or therapeutic ratio is the ratio between the concentration causing a toxic effect and the concentration causing a therapeutic effect

•  It is a measure of a drug‘s safety

Page 19: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Human Toxicity

•  Definition of acute LD50 in human not helpful – it is generally not experimentally accessible

•  A lethal dose has to be avoided at all costs

•  For a safe drug, we need to achieve less than 1 death per million, i.e. LD0,000001

•  Apart form acute toxicity, long-term effects are of great importance

–  Mutagenicity

–  Carcinogenicity

–  ...

Page 20: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Poison/Drug •  Poisons obviously have a biological activity

•  We can thus apply the same principles as for pharmaceutical activity

–  Toxicokinetics

–  Toxicodynamics

•  In principle, all of the methods described to model biological activity are applicable as well

•  Problem:

–  Toxicity is often not a single, well defined process (in contrast to binding, activation, ...)

–  What is the mechanism? Where to start?

Page 21: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Types of Toxicity

• Acute toxicity –  Exposition to a single dose or multiple

doses in a short space of time –  Symptoms occur immediately or briefly

after exposition

• Chronic toxicity –  Prolonged exposition to low-level doses –  Slow accumulation of the poison to toxic

concentrations –  Often due to lack of excretion/elimination

Page 22: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Classification of Poisons

• Target organ (liver, kidneys, ...)

• Application (pesticide, solvent, food

supplement, ...)

•  Source (animal or plant poisons,

synthetic, ...)

•  Effect (cancer, mutagenesis, liver

damage, kidney failure, ...)

Page 23: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Exposition to Poisons

•  Environmental exposition is a common source

•  Exposition to toxic substances is controlled by legislation –  Short-term exposure limit (STEL) [in Germany:

MAK (maximale Arbeitsplatzkonzentration)]

•  However:

Carcinogenic substances are never harmless!

Even smallest amounts can cause genetic alterations.

Page 24: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Molecular Toxicology

•  Studies the interaction of a poison with a

biological object

•  Consider the effect on a molecular level

•  Becoming increasingly important as the

mechanisms of toxic action of compounds are

becoming known

•  Obviously of the utmost importance in the

drug design process

Page 25: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

What causes toxicity?

Many different mechanisms involved: •  Biotransformation (metabolization) •  Interactions between several

substances which are not toxic by themselves (at the individual doses)

•  Inhibition/inactivation/denaturation of proteins (enzymes, receptors, ...)

•  Saturation of metabolism •  Activation/blocking of receptors •  ...

Page 26: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Paracetamol •  Very common analgesic and antipyretic

(Acetaminophen)

•  Normal dose: 500-1000 mg

•  Usually well tolerated

•  But: high doses can be toxic!

•  Doses of 10 g/day or more lead to severe live cell necrosis (often lethal)

•  The effect is caused by a toxic metabolite of paracetamol, N-acetyl-p-benzoquinoneimine

The dose makes the poison

Paracetamol (Acetaminophen)

Page 27: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Paracetamol

•  Damage to liver cells is caused by highly reactive metabolites

•  Formed by cytochromes, their reaction with proteins in the liver causes the toxic effect

•  Low doses: metabolites are captured and detoxified by glutathione by forming harmless conjugates

•  Toxic dose: –  Glutathione storage exhausted

–  Metabolites cannot be detoxified

Glutathione

Page 28: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Paracetamol

•  Stimulation of chytochrome p450 lowers the glutathione level

•  Some therapeutically active compounds activate p450 (strongly)

•  Consequence: even very low (normally non-toxic) doses of paracetamol become toxic

•  Toxic doses well below 6 g •  Problematic for patients with pre-existing

damage to the liver (alcohol abuse!) ) Interaction with other substances can cause toxicity!

Page 29: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Drug Interactions

•  Example: administration of phenytoin (an

antiepileptic) and salicylic acid at the same time

results in abnormally high plasma levels

•  Problem: both drugs are eliminated through the same

enzyme

•  Consequence: saturation of the enzyme reduces

elimination rates

•  This can lead to toxic effects, as the effective plasma

concentration is much higher than anticipated

Drug interaction by saturation of an enzyme!

Page 30: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Benzene/Toluene

•  Benzene has a high acute toxicity and is also carcinogenic – in contrast to structurally very similar toluene

•  Structures differ only by a single methyl group

•  Benzene is easily absorbed, also across the skin

•  It is also easily excreted again, mostly through the lung

•  About half of the absorbed amount is typically metabolized

•  Toxic effect is most likely due to this biotransformation

Benzene

Toluene

Page 31: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Benzene

Acute toxicity

•  More than 0.5 ml/kg causes

–  Intoxication

–  Headaches, dizziness

•  Higher doses:

–  Convulsions

–  Unconsciousness

–  Cardiac arrhythmia

–  Eventually death by central respiratory paralysis

Page 32: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Benzene

Chronic toxicity or massive single doses:

•  Hemotoxicity –  Inhibition of erythropoiesis, leukopoiesis and

thrombopoiesis

–  No therapy known

•  Carcinogenicity –  Leukemia

–  Causes irreversible chromosomal aberrations in lymphocytes and bone marrow cells

–  Benzene is one of the most important environmental poisons

Page 33: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Metabolization of Benzene

•  Initial step: enzymatic epoxidation

•  Epoxides are highly reactive

•  Can react with hydrogen atoms of biological

macromolecules

•  Carcinogenic and mutagenic effects is

(probably) caused by reactions with nucleic

acids

•  Toluene is metabolized differently (starting

with the methyl group) and is thus much less

toxic

Mono- oxygenase

Page 34: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Carcinogens

•  In animal models, symmetric dialkylnitrosamines cause

–  Liver tumors after chronic exposure to low doses

–  Kidney tumors after exposure to a single high dose

•  Small amounts of nitrosamines are very common (in particular in alcoholic beverages, certain meat products)

•  Also formed endogenously (production of nitrite from saliva and gastric juice)

Dimethylnitrosamine

Page 35: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Carcinogens •  Polycyclic aromatic hydrocarbons

(PAHs) are often carcinogenic

•  Effect is again caused by

metabolites

•  Some of these metabolites show

acute gene toxicity

•  They have also been shown to

react with DNA in vivo

•  Bay region is important for

metabolic activation

Benzo(a)pyren

1,2-5,6 Dibenzanthrazen

Page 36: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Metabolization

Metabolization of benzo(a)pyrene to a diol epoxide, which then reacts with the exocyclic amino group of guanine

Page 37: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Testing Prevents Disasters •  No or insufficient testing of novel pharmaceutical

compounds led to several major disasters –  Brain damage and death in small children due to

sulfonamides (late 1930s) –  More than 100 deaths through diethylene glycol used as a

solvent for sulfanilamide (this incident led to the foundation of the Food and Drug Administration [FDA] in the USA)

–  Severe birth defects after the use of thalidomide during pregnancy in about 10,000 children worldwide

•  High standards for drug safety have drastically reduced these incidents

•  Nevertheless, drugs are taken off the market again because long-term (side) effects have not been recognized early on

Page 38: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Models: Animal Models

•  How to test for human toxicity early on?

•  Difficult: there is rather little toxicological data

available for humans (systematic toxicological testing

with human subjects is not considered acceptable!)

•  The vast majority of reliable data thus stems from

animal experiments

•  As we have seen before, these data are often hard to

transfer to humans

•  But: better than nothing!

Page 39: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Animal Models

•  Animal experiments are...

–  Expensive

–  Time-consuming

–  Raise ethical issues

–  Required by law

•  Reduction of animal use by

–  In vitro models

–  Computational models

http://abclabs.com

Page 40: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Animal Use

•  Strong growth of animal use between 1945 and 1968

•  Stagnation until the middle of the 70s, then steady decrease (1978-1988 decrease by 60% in West Germany)

•  Reduction quite remarkable: more substances tested than ever!

•  Key reason: in vitro tests (Ames test)

•  Theoretical models still play a very minor role

Page 41: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Animal Use 1991-1995 Species 1991 1992 1993 1994

Mouse 1.223.741 1.064.883 973.106 868.312

Rat 611.530 558.516 508.769 459.781

... ... ... ... ...

Total 2.402.710 2.082.588 1.924.221 1.758.500

Quelle: Bundesministerium für Verbraucherschutz, Information Nr. 44 v. 30. Oktober 1995 http://www.bmelv.de/cae/servlet/contentblob/765788/publicationFile/43424/2008-TierversuchszahlenGesamt.pdf

•  About half of them are related to medical research

•  Most of them are rodents (mice, rats)

•  Over the last decade the number of animals used in animal experiments has been increasing steadily (2008: 2.6 mio. in Germany)

•  Number for mice are always increasing, most other species going down

•  About 171,000 are currently being used per year for toxicological studies

Page 42: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Comparison between Species •  Different species may react very differently to the same drug

•  Example: lysergic acid diethylamide (LSD)

–  Experiment: administer a hallucinogenic, but subtoxic, dose to a male Asiatic elephant

–  Estimate: dose of 0.3 g

(about 0.06 mg/kg)

–  Result: Death.

) Toxic dose for an

elephant about 1000

lower than for a mouse!

West LJ, Pierce CM, Thomas WD. Lysergic Acid Diethylamide: Its Effects on a Male Asiatic Elephant. Science. 1962 Dec 7;138(3545):1100-1103.

Page 43: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Transferability of the Data

Toxicity of LSD

Species LD50 [mg/kg]

Mouse 50-60

Rat 16.5

Rabbit 0.3

Elephant << 0.06

Human >> 0.003

Page 44: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Transferability of Data

•  Example: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, “Seveso poison”)

•  Even in the closely related species hamster and guinea pig toxicity differs by three orders of magnitude

•  Extrapolation is thus very, very dangerous!

•  Even data from close relatives can be misleading: apes are rather insensitive to TCDD

Page 45: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Models: in vitro Tests

•  Example: Ames test identifies cpds with mutagenic (and carcinogenic) potential

•  Carefully engineered strain of Salmonella typhimurium

•  Lacks the ability to synthesize His •  Incubated together with the compound and a few

other things (e.g., liver extract to check for mutagenicity of possible metabolites)

•  Mutagenic agent can cause backmutations that can grow into larger colonies

•  Colony count is a measure for mutagenic potential Ames, B., F. Lee, and W. Durston; Proc. Natl. Acad. Sci. USA 70:782-786, 1973

Page 46: Drug Design 2 - uni-tuebingen.deabi.inf.uni-tuebingen.de/Teaching/.../DD2/Slides/DD2_WS09_12_ADMET.pdf · Drug Design 2 Oliver Kohlbacher Winter 2009/2010 12. ADMET . Overview •

Problems Predicting Toxicity

•  Wide range of biochemical processes involved

•  Very similar structures have very different toxicological properties (structure-toxicity landscape is very rough)

•  Different mechanisms can result in the same toxicological outcome

•  Very different structure-activity relationships between different classes of compounds

•  Often caused by metabolites, so not a property directly related to a compound‘s structure!

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Theoretical Models

Which approaches are there?

•  Knowledge-based (“expert systems”)

–  Store expert knowledge in as individual rules

–  Applying these rules to a given structure results in a classification

•  Statistical models ((Q)SAR)

–  Automated statistical analysis of large-scale data sets using statistical methods

–  No experts required, but strongly dependent on data quality, inclusion of all relevant processes

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Top-down/Bottom-up

Richard, Toxicol Lett 102-103:611-616, 1998

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What is being modeled? •  There is not an single toxicity model, but

numerous different toxicological properties are being modeled independently: –  Liver toxicity

–  Kidney toxicity

–  Carcinogenicity

–  Mutagenicity

–  Reproductive toxicity

–  Acute LD50 (rat)

–  Transdermal absorption

–  ...

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Approaches Statistical Approaches

•  CASE/MultiCASE

Klopman; J. Am. Chem. Soc 106:7315-7321, 1984

Klopman; QSAR 11:176-184, 1992

•  TOPKAT

Enslein et al.; Mutat. Res. 305:47-61, 1992

Expert Systems

•  DEREK

Sanderson, Earnshaw; Human Exp. Toxicol. 10:261-273, 1991

•  ONCOLOGIC

Woo et al.; Toxicol. Lett. 79:219-228, 1995

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Prediction Models

Richard, Toxicol Lett 102-103:611-616, 1998

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Example: DEREK

•  DEREK is a knowledge-based system (Deductive Estimation of Risk from Existing Knowledge)

•  Based on a program for organic synthesis planning (LHASA)

–  Rather old(1980 bzw. 1985)

–  Developed for VAX

–  600 modules in Fortran, C and Macro

–  Rule-description language CHMTRN

•  Extends LHASAs rule language for elements required in toxicology (DERTRN)

•  Initially about 50 different rules

„...based on a combination of over 30 years experience of toxicological work...“

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DEREK •  Simple rules of the structure IF structural chemical property THEN specific outcome possible

•  Results are purely qualitative (!) •  In addition, it contains the FDA‘s rule

set for carcinogenicity • Mainly used to select compounds in a

campaign, remove those with obvious problems

•  Also used as an indicator where additional experiments are required

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DEREK Rules

Four sections

1.  Descriptions

2.  Usage information

3.  Structural pattern

triggering the rule

4.  DERTRN query to refine

the structural pattern

further

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DEREK: Pros/Cons

+ Development of rules is overseen by the users and transparent to them – there is always an explanation for a rule

+ New rules can be integrated rather simply

+ Simple user interface

-  Rule syntax rather limited, no 3D definitions

-  Rules are rather coarse and capture only a few key metabolic mechanisms

-  Inclusion of toxicological databases and the knowledge therein might improve predictions

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Example: (Multi)CASE

•  CASE - Computer Automated Structure Evaluation

•  Has been extended into Multi-CASE

•  Relies on statistical analysis of a training data set combining compound structure and their biological activity

•  Training data set must contain a broad range of different structures and toxicological endpoints

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CASE: Training Data

•  Training data set: relates structures to biological/toxicological activity

•  Activity is given in ‘CASE units’ 10-19: inactive 20-29: weak activity 30-99: active

•  Structures is given as SMILES, KLN, or as a MOL file

•  Analysis is based on heavy atoms alone

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CASE: Training Data •  Training data set has to be examined thoroughly to

ensure even coverage of chemspace

–  Check for overrepresented structures

–  Identify important missing structures/mechanisms

•  As many data points as possible should be included

•  Data of very similar cpds. with identical mechanisms can be pooled

•  Problem: each change in the data set leads to a different predictive model

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CASE: Model Construction

•  Decompose all structures into fragments of

size 2 – 10

•  Classify fragments as

–  Biophores/toxicophores (statistically active)

–  Biophobes (statistically inactive)

•  Compute physicochemical descriptors and 2D

descriptors for a QSAR analysis

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CASE: Classification

• Many fragments are not by themselves

determining factors for toxicological

activity

•  Assumption: binomial distribution of all

fragments within a class

•  Statistically significant deviation from

this distribution fragment is relevant

for activity

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CASE: Prediction

•  Two steps: –  Activity prediction –  Estimation of toxicity

•  Input structure is decomposed into fragments

•  Comparison of fragments to biophores/biophobes

•  Prediction of activity likelihood based on these matches

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CASE: Prediction

•  Toxicity estimation uses QSAR •  Model based on multivariate analysis •  Forward selection of descriptors •  Initial descriptors

–  Biophores –  Biophobes –  Predicted log P

•  Descriptors are added until the model does not improve

•  All standard caveats discussed earlier in the lecture of course apply!

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Multi-CASE

•  Aims at reducing problems caused by highly correlated descriptors

•  Solution: several stepwise CASE predictions –  Predict strongest biophore

–  Remove molecules containing this biophore from the training data

–  Repeat until the training data set is empty or no significant improvement can be reached

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Multi-CASE

•  Distinguishes between activity and modulation of activity –  Split training data set into different classes, based on

presence or absence of a biophore –  Conduct a QSAR analysis in each of the classes to

determine whether related biophores lead to an increase/decrease in activity

•  Uses a larger number of descriptors than CASE •  Prediction:

–  Search for biophores in the input structure –  For each biophore identified, search for modulating

biophores

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Multi-CASE: Pros/Cons

+ Predictive models do not require prior

(expert) knowledge

+ Quantitative prediction

-  Prediction accuracy critically dependent on

the quality (and manual curation) of the

training data set

-  Output often ambiguous expert needed!

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Multi-CASE vs. DEREK

Prediction accuracy [%]

DEREK 59

Multi-CASE 49

COMPACT 54

TOPKAT 57

Greene; ADDR 54:417-431, 2002

Prediction of carcinogenicity of 44 compounds

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Multi-CASE vs. DEREK

DEREK 4.01 Multi-CASE 3.45

Sensitivity 45% 30%

Specificity 62% 84%

Concordance 60% 79%

Greene; ADDR 54:417-431, 2002

Prediction of Ames test results for 974 cpds.

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State of the Art – 1990

•  In 1990 Tennant et al. asked several experts in

toxicology to predict carcinogenicity for 44

compounds

•  Computational methods were applied in parallel

•  After experimental testing, the following results

were obtained in 1993:

–  Best result: expert (80% correct)

–  Theoretical approaches: 45-65% correct

•  Results hardly better than random!

•  Not good enough to replace animal models! Tennant et al.; Mutagenesis 5:3-14, 1990

Ashley, Tennant; Mutagenesis 9:7-15, 1994

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State of the Art – 2003

•  Predictive Toxicology Challenge: Competition to assess the quality of modern in silico methods

•  Machine learning

•  Limited to the prediction of carcinogenicity

•  Fourteen teams contributed predictions

•  111 models

•  Result: five(!) models performed better than random

Tuivonen et al.; Bioinformatics 19(10):1183-1193, 2003

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State of the Art – 2009

•  Valerio et al. (FDA) examined two popular state-of-the-art software packages

–  LMA (Leadscope Model Applier)

QSAR/data mining approach based on structural features

–  MC4PC (a MultiCase descendant)

Rule-based and QSAR approach

•  An external dataset of 43 phytochemicals with known rodent carcinogenicity was used to validate the predictions

Valerio et al., Mol. Nutr. Food Res., 54:1-9 (2010) Yang et al., Toxicol. Mech. Methods, 18:277-295 (2008)

Matthews et al., Toxicol. Mech. Methods, 18:189-206 (2008)

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State of the Art – 2009

•  Results: comparable for both programs

•  High specificity, low sensitivity

•  Still not very convincing

•  Combination of both codes into a consensus leads to even worse predictions

Valerio et al., Mol. Nutr. Food Res., 54:1-9 (2010)

MC4PC LMA

Specificity 94% 59%

Sensitivity 47% 50%

False positives 6% 41%

False negatives 53% 50%

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Are predictions possible?

•  At the moment predictions are not sufficiently

reliable

•  Even modern statistical learning methods fail to

capture the full complexity of toxicology

•  Without human experts and experimental testing, no

reliable statement on a compound’s toxicity is

possible

•  Nevertheless:

–  Good tool for the expert to guide toxicological studies

–  Can yield important hints for an early selection of

candidates

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Summary •  Bioavailability is an essential property for a drug

•  In silico predictions are possible, although difficult using QSAR approaches

•  All drugs have toxic side effects

•  Important is the therapeutic index

•  Prediction is very difficult due to the complexity of toxicological mechanisms

•  in vitro and in silico approaches still cannot replace animal models

•  In silico toxicity predictions: knowledge/rule-based and statistical approaches are currently in use

•  Predictions are still not reliable enough, although they are being used to guide decisions

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References Books •  [BKK] Böhm, Klebe, Kubinyi: Wirkstoffdesign, Spektrum 2002 •  Mutschler: Drug actions. Basic Principles and Therapeutic

Aspects, Medpharm Scientific Publishers; Auflage: 6Rev Ed (1994)

•  Klaassen: Casarett and Doull's Toxicology: The Basic Science of Poisons, Mcgraw-Hill Professional; 7th revised ed. (2008)

Papers •  Valerio LG Jr, Arvidson KB, Busta E, Minnier BL, Kruhlak NL,

Benz RD. Testing computational toxicology models with phytochemicals. Mol Nutr Food Res. 2009 (Epub ahead of print), PMID: 20024931