Pharmacogenomics:

an overview

Dr. dr. Mgs. Irsan Saleh, M.Biomed

Dept of Pharmacology
Faculty of Medicine Sriwijaya University
irsan_saleh_hasani@yahoo.com
 Interindividual variability in drug response
Disease Drug Class Rate response (%)
Asthma β-agonists, others 25-60
Solid cancer various 0-30
Depression SSRIs, tryciclic, others 60-80
Diabetes Sulfonylurea, others 25-50
Arthritis NSAIDs, COX-2 50-80
inhibitors, others
Migraine Triptan, NSAIDs, ergot 40-70
Schizoprenia Various 25-75
Major drug Various 2 million hospitalized
toxicity patients/y, 4th-6th leading
cause of death in US
1994
 Factors contributing to interindividual
variability in drug response

• Age
• Environmental
• Weight
• Gender
• Concomitant Diseases
• Concomitant Drugs
• Social factors
• Genetics
 Definition

Pharmacogenomics

Pharmacon Genome

The chemical substance that The entire DNA content of a

influence biological function cell, including all of genes
at molecular, cell or organs of and all of the intergenic
organism. regions.

The study of genome-derived data, including human genetic

variation, RNA and protein expression differences, to predict
drug response in individual patients or groups of patients.
Other definition

• The application of genome science

(genomics) to the study of human
variability in drug response.
• The study of genetic content (DNA
sequence) of humans for drug
discovery & optimization.
• Refer to the general study of all many
different genes that determine drug
behavior.
 History

1. Vision and some predictive observations

• Garrod (1902) : alcaptonuria and
phenylketonuria due to biochemical
individuality.
• Snyder (1932) : a heritable disability to
taste phenylthiocarbamide.
• Savin & Glick (1943) : a genetic lack
atropine esterase in some rabbits.
 History (cont. …)

2. Pharmacogenetics lives: systemic case studies

• 1950 : several observation indicated clearly the
dependence drug effects on the genetic constitution.
• Variation in isoniazid acetylation
• Variation in cholinesterase activity
• Hemolysis cused deficiency G-6-PD
• Motulsky (1957) : Drug reaction, enzymes and
biochemical genetics
• Vogel (1959) : coined the Pharmacogenetics
• Kalow (1962) : summarized all available knowledge
in a book
 History (cont. …)
3. Broadening of pharmacogenetic knowledge
• Manya centers contributed new data, but data
represented monogenic variations.
• Weber’s book (1997) : listed 15 variable metabolizing
enzymes, 11 variable drug receptors, 14 other variable
• Kalow (2001) : counted 42 variable drug-metabolizing
enzymes
• The enzyme’s variation are complex: mutations,
spicing defects, gene deletion, present or stop
codon.
• Many clinical case study due to enzyme’s
variation reported and genetic failure of drug-
metabolizing enzyme’s can lead to a patient’s
death.
 History (cont. …)
4. Pharmacogenetic differences between population
• Paskind (1921): atropine sulfat caused a initial
slowing of heart rate in Caucasian (20) but not
African-American subjects.
• Chen & Poth (1929): variation in pupillary size after
applying mydriatic eye drop (increase largest in
Caucasian, intermediate in Asians and smallest in
African American).
• Sunahara et al. (1961): Genetical and geographical
studies in isoniazid inactivation.
• Beutler (1993): primaquine caused hemolysis on
African soldiers due to deficiency G6PD
• Kalow (2001): 11 mutations of CYP2D6 was tested :
European carried 7, Chinese 4, Japanese 3 and
Africans 2.
 History (cont. …)

5. The rise of multifactorial pharmacogenetics

• Differences between people in their response to

drugs are regular occurrences.
• The causes of most differences generally remain
uninvestigated, but the presence of both genetic
and environmental cause is common.
• It is of considerable interest to know the relative
contribution of the two causes.
• Kalow et al. (1999; 1998) : assess the genetic
component in pharmacological variability
 History (cont. …)

The proportion of the disease that is due

to genetic factors

Huntington's
Disease

Schizophrenia
Genes
Environment
Rheumatoid
Arthritis

HDL level

0% 50% 100%
 History (cont. …)

6. Advances in molecular biology

1967 Gilbert discovered DNA ligase

1972-73 DNA cloning techniques established by
Boyer, Cohen and Berg
1988 The first biothechnology products appear.
These were tissue plaminogen factor, α-
interferon, human insulin, human growth
factors and erythropoetin.
1990 Human genome project was initiated and
finished at 2003
7. Pharmacogenomics and Pharamacogenetics

Pharmacogenomics :
• the use of genetic content (DNA sequence)
of humans for drug discovery & optimization
• refer to the general study of all many
different genes that determine drug behavior
Pharmacogenetics :
• the use of genetic content of humans to
understand drug effects.
• refer to the study of inherited difference
(variation) in drug metabolism & response

Drug Effects Pharmacogenetics Drug Metabolism

• Deficiency of G-6-P • Slow & rapid acetylation

dehidrogenasi  sulfonamide Genetics of INH
• High activity cholinesterase • Poor & large hydroxylation
 succinylcholine of Debrisoaquin

Drug respons

Environment Diet Lifestyle State of health

 Drug discovery and development in genomics era

Pharmacogenomics ►
DNA Genomics
mRNA Transcriptomics
Protein Proteomics
Drug respons
Protein-complex Functional Proteomics
Metabolites Metabolomics
F • Drug discovery & development
Cell level • Identification & validation of
l
u new drug targets
i Tissue level
• Modeling of disease progression
d • Identification of novel
s Organ level diagnostic or prognostic markers
• Pathogenesis of diseases

High-throughput technologies System Biology

Robotics & Bioinformatics

 Pharmacogenomics

DRUG
DRUG DRUG
METABOLIZING
TARGETS TRANSPORTERS
ENZYMES

PHARMACODYNAMICS PHARMACOKINETICS

Variability in
Efficacy/Toxicity
Johnson JA. Trends in Genetics 2003: 660-666
Drug Transporter
 Drug Transporter (cont. …)

1. Drug transporters such as ABCB1, ABCC1, ABCC2,

ABCC3 participate in opioid transport and influence
opioid efficacy and side effects.
2. Substrates of ABCB1/MDR1 include morphine,
methadone, fentanyl, sufentanil, alfentanil, and
morphine-6-glucuronide and anticancer
3. Other transporters potentially involved in opioid
distribution are MRP1, MRP2, and MRP3 (ABC
transporter subfamily C), organic anion transporters
(OAT1 and 3), and organic anion transporter
polypeptides (OATP1 and 2, solute carrier family 21).
Drug Metabolizing Enzymes
 Examples of Drug Metabolism Pharmacogenomics

NEJM 2003; 348: 529-537

 Examples of Drug Metabolism Pharmacogenomics

NEJM 2003; 348: 529-537

Nortriptyline kinetics and CYP2D6 genotype
(Dalén et al 1998)

CYP2D6
Nortriptyline 10-OH-nortriptyline
Examples of Drug Target Pharmacogenomics

Evans WE. NEJM 2003; 348:538-48

 Beta-blockers and
Hypertension (HTN)
• HTN is the most prevalent chronic disease in the
US and a contributor to morbidity and mortality
• Beta-blockers are first-line agent in the treatment
of HTN
• Marked variability in response to beta-blockers
– 30-60% of patients fail to achieve adequate blood
pressure lowering with beta-blockers
• Common beta-blockers used in HTN:
– Metoprolol
– Atenolol
 Beta-1 Adrenergic Receptor

Codon 49 SerGly

Codon 389
ArgGly

Podlowski, et al. J Mol Med 2000;78:90.

Beta-1 Receptor Polymorphisms and Response
to Metoprolol

Johnson JA et al. Clin Pharmacol Ther 2003; 74:44-52

 Beta-2 Adrenergic Receptor Polymorphisms
and Response to Albuterol in Asthma

• Hyperreactivity of the airways is the hallmark of

asthma
• Airway smooth muscle contains beta-2 receptors
that produce broncodilation
• Albuterol is a beta-2 agonist that is used in the
treatment of asthma
– Produces smooth muscle cell relaxation and
bronchodilation
• Forced expiratory volume in 1 second (FEV1)
– Phenotypic measure of response
 Beta-2 Polymorphisms and
Response to Albuterol
•Single 8 mg albuterol dose

•Albuterol-evoked increases
in FEV1 were higher and
more rapid in Arg16
homozyotes compared with
Gly carriers

• Codon 16 polymorphism is
a determinant of
bronchodilator response to
albuterol

Lima JJ et al. Clin Pharmacol

Ther 1999; 65: 519-25
Lima JJ. Clin Pharmacol Ther 1999; 65:519-25
 Codein Pharmacogentics
N CH3
• Ultrarapid metabolizers
CH2 CYP2D6 (UMs)
• Extensive metabolizers
CH2 (EMs)
CH3O O OH
• Poor metabolizers (PMs)
Codein
N CH3 N CH3

CH2 CH2

CH2 CH2

CH3O O Glucuronate HO O OH
N CH3 N CH3
Morphine
Codein-6-glucuronate CH2 CH2

CH2 CH2

Glukuronate O OH OH O Glucuronate

Morphine-3-glucuronate Morphine-6-glucuronate

Drug transporter
Genetics polymorphism
Opioid receptor in brain
 Appling pharmacogenomics in drug discovery
and development

Discovery Exploratory Development Full Development

Phase I Phase II Phase III Phase IV

0 5 10 15
Years

11-15 Years

Idea Marketed Drug

Disease Target Selecting Pharmacogenetics
genetics variability responsders

Choosing the Better Improving Predicting

best targets understanding early decision efficacy and
of our Targets making safety
Choosing the best targets &
better understanding targets
 Drug discovery and development in genomics era

Pharmacogenomics ►
DNA Genomics
mRNA Transcriptomics
Protein Proteomics
Drug respons
Protein-complex Functional Proteomics
Metabolites Metabolomics
F • Drug discovery & development
Cell level • Identification & validation of
l
u new drug targets
i Tissue level
• Modeling of disease progression
d • Identification of novel
s Organ level diagnostic or prognostic markers
• Pathogenesis of diseases

High-throughput technologies System Biology

Robotics & Bioinformatics

 Identify disease

Find a drug effective

against disease protein
Isolate protein (2-5 years)
involved in Scale-up
disease (2-5 years)

Preclinical testing
(1-3 years) Human clinical trials
(2-10 years)

Formulation

FDA approval
(2-3 years)
 Choosing the best targets
Drugs
Genomics
DNA Proteomics PROTEINS DRUGS
(cf. EPO, Interferons, …)
Protein GENETICS
PHYSIOPATHOLOGY ANTIBODY DRUGS
(in vitro, in vivo, ..)

SMALL MOLECULES
DRUGS
FUNCTIONAL DRUG RATIONAL DRUG
VALIDATION DISCOVERY DESIGN
STRUCTURE-BASED
DRUG DESIGN
• AS DRUGS (incl. in silico…)
• AS TARGETS
HIGH THROUGHPUT
SCREENING

- RELEVANT ASSAYS…
- VERY LARGE LIBRARIES
OF COMPOUNDS
(SYNTHETIC OR NATURAL)
“INVENTORY”
Improving early decision making
• Phase I studies
– Explain outliers or patient-to-patient
variability in PK
– Exclude or include specific patients
– Normalize genotype frequencies
– Bridge to other populations
 Example: Desipramine PK Parameters

Genotyping can increase trial safety and explain outlying data

Drug interaction study

50
CYP2D6 *6/*9 • CYP2D6 poor metabolizers
(2 null alleles) excluded.
40
• One outlier with slow
t1/2, hr

metabolism
30
• Outlier has *6 null allele and *9
allele with reduced enzymatic
20 activity.
• Expected occurrence of null/*9
10 Katz et al., Abbott Labs.
genotype is 0.4%
• Phase II/III studies
– Identify genetically-defined groups with more
pronounced or rapidly progressing disease
– Exclude/include at-risk individuals
– Stratify studies based on genotypes
• Clinical response
• Risk of adverse events
– Where appropriate, develop drugs for specific
groups
– Identify genetic markers associated with clinical
outcomes
"Here's my
sequence..."

The New Yorker