Personalized Medicine

Towards
Personalized
Medicine
Michel Dumontier, Ph.D.

Assistant Professor of Bioinformatics
Department of Biology, Institute of Biochemistry, School of Computer Science
Carleton University
Ottawa Institute for Systems Biology

Ottawa-Carleton Institute for Biomedical Engineering
Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Drug Development Life Cycle
Discovery
Preclinical Testing
(Lab and Animal Testing)
Phase I
(20-30 Healthy Volunteers used to
check for safety and dosage)
Phase II
(100-300 Patient Volunteers used to
check for efficacy and side effects)
Phase III
(1000-5000 Patient Volunteers
used to monitor reactions to
long-term drug use)
FDA Review
& Approval
Post-Marketing
Testing
Years
0 2 4 6 8 10 12 14 16

Drug Discovery aims to identify a
lead compound
• Discovery:
– Identify the molecular target
– Design an assay for regulation of activity
– Identify hits with chemical screening
– Determine mechanism of action
– Identify a lead compound with strong binding
affinity, KD < 1μM
– Demonstrate therapeutic value with in vivo proof of
concept in animals/cell cultures

The development phase evaluates
drug effectiveness
• Drugs must overcome numerous challenges
– chemically stable in stomach (pH 1)
– not digested by gastrointestinal enzymes
– absorbed into the bloodstream
• pass through series of cell membranes
– not bind tightly to other substances
– survive xenobiotic detoxification by liver enzymes
– avoid excretion by kidneys
– brain: cross blood-brain barrier (blocks polar substances)
– intracellular receptor: pass through cell membrane

Adverse Drug Reactions
Known side effects Medication Product quality
Unavoidable Avoidable errors defects
Preventable
adverse
events
Remaining
uncertainties
• Unexpected side effects
Injury • Unstudied uses
or death • Unstudied populations
• ADR is one of the leading causes of hospitalization and death

• 6.7% of hospitalized patients have serious ADRs
• 0.3% of hospitalized patients have fatal ADRs

LIPITOR:
Known Side Effects
• Lipitor blocks the

production of
cholesterol in the body.
• May reduce risk of

hardening of the
arteries, which can lead
to heart attacks, stroke,
and peripheral vascular
disease

VIOXX: Unknown Side Effects
Treatment for Acute Pain
increased risk of heart attack and stroke

(after 18 months)

Drug Recalls
400
Number
200
226
248
176
352
156
254
191
316
248
354
34
88
72
72
60
53
83
88
0
1995 1996 1997 1998 1999 2000 2001 2002 2003
Fiscal year
FDA: Center for Drug Evaluation and
Prescription Over-the-counter
Research 2003 - Report to the Nation Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Cost of developing drugs
• Global Alliance for Tuberculosis Drug
Development
– www.tballiance.org
– "The Economics of TB Drug Development"
• Costs to discover and develop a new anti-
TB drug range from $115 million to $240
million.
– $40 million to $125 million for discovery
– $76 million to $115 million for preclinical
development through Phase III trials

Drug Development & Costs
COST # Drugs %Total
• Discovery $100M 2000 100%
• Pre-Clinical $0.5M 100 5%
• Phase I $0.5M 20 1%
• Phase II $5M 3 0.15%
• Phase III $50M 2 0.10%
• FDA 1 0.05%
~$156M

R&D Spending and New Medicines
• 38 new medicines in
2004
– Cancer
– Infectious diseases
– Parkinson’s therapy
– Radiation contamination
– Pain alleviation from
made from a synthetic
form of a sea-snail
venom.
PhRMA Annual Report 2005-2006 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

An Analysis
• National Institute for Health Care Management
– Changing Patterns of Pharmaceutical Innovation,
May 2002
• Quality of pharmaceutical innovation varies

widely.
– Breakthrough treatments for life threatening
diseases
TO
– Minor modifications of drugs that have been on the
market for some time.

Most drugs approved are only
slightly modified
Other
11%
IMD
54%
NME
35%

Less innovative than you think

The Hatch-Waxman Act (1984)
• Drug Price Competition and Patent Term
Restoration Act
• Open the market to generics immediately after patent
expiry, but new tactics to protect
– Easier for generics to obtain FDA marketing approval
• Drug Company
– 30-month stay against generic manufactures that challenge
their patents.
– Additional period (< 5 yrs) of marketing exclusivity in addition
to 20 year patent exclusivity
– Easy patents for drug variants
• keep generics off the market by protecting their drugs with extra
patents of poor quality, filing lawsuits to protect the patents even when
the lawsuit will be lost, but getting the extra market exclusivity anyway.

Profits as a Percentage of Assets, 2002
Top 7 of Fortune 500 Industries
Pharmaceuticals 14.0%
Household Products 10.7%
M edical Products & Equipment 9.5%
Food Services 9.3%
Publishing, Printing 8.2%
Apparel 7.5%
Consumer Food Products 7.2%
0% 2% 4% 6% 8% 10% 12% 14% 16%
Source: Fortune Magazine, April 14, 2003

The Drug Business
• Drug development has been and still is
costly, risky, and lengthy
• R&D costs have increased, but the
industry remains one of the most profitable
• Pharmaceutical innovation is targeted
towards protecting interests
• The payoffs for improvements in the
process are significant

Agouron Pharmaceuticals
• Designed a non-peptidic
hydroxamate inhibitor
• Used structure of
recombinant human MMPs
bound to various inhibitors
• Determined key residues,

ligand substituents needed
for binding Gelatinase A

MMPI in Cancer Therapy
• Design of inhibitors
• Matrix Metallo Proteinase Inhibitors (MMPI) are

a class of cancer therapeutics
– MMP levels are increased in areas surrounding tumor
– Degrade extracellular matrix proteins and can lead to
spread of cancer
– Inhibitors
• can prevent metastasis
• may also play role in blocking tumor growth
Melissa Passino. Structural Bioinformatics in Drug Discovery.

MMP catalysis
“metallo” in MMP = zinc
→ catalytic domain contains 2 zinc atoms
Whittaker et al. Chem. Rev. 1999, 99, 2735-2776

Peptidic hydroxamate inhibitors
• Specificity for
MMPs over other
MPs
• Better binding
• But poor oral

bioavailability

Finding drug leads
• If we have a target, how do we find some
compounds that might bind to it?
• Classic: exhaustive screening
• Modern: computational screening!

Combinatorial Chemistry
• Parallel synthetic approach

– Build on previous products
– Generate diversity by adding R
groups
– Recover most active compounds
• Solid phase synthesis
– Wash away excess reagants &
other products
– Can recover the main product
• Parallel testing

combinatorial synthesis of non-peptide
drugs
1) H
HO O R N O
NH2
RXN 1
+ R
Bead NH2 NH2
Bead
2) H
R N O H
R N O
O
RXN 2
+ O
Bead NH2 Cl R
Bead N R
H
Structure-Based Docking Methods
• Need 3D structure
• Scan a virtual library of small molecules and “dock” them to a site
of interest on a protein structure
• Predict binding energy
• Filters thousands of compounds relatively quickly
• Top hits can be used for more rigorous computational/experimental
characterization and optimization

Importance of Structural
Bioinformatics
• Provides a framework for
understanding general
macromolecular features
– Automatic identification of binding
pockets.
– Measurement size of surface binding
pockets.
• Speeds up key steps in drug

discovery
– Understand molecular basis for disease
– Determine potential interactors
– Identify potential targets which bind small
molecules.

Structural bioinformatics to design
nonpeptidic hydroxylates
oral anti- anti-

binding
bioavailabity growth metastasis
repeat…

Prinomastat
• Good oral
bioavailability
• Selective for specific
MMPs
• Evidence showing
prevention of lung
cancer metastasis in
rat and mice models
• Clinical trials
– cell lung cancer
– prostate cancer

“If it were not for the great
variability among individuals,
medicine might as well be a
science and not an art”
Sir William Osler, 1892

Major sources of variation
• Single Nucleotide Polymorphisms (SNPs)
– Single base change in DNA
AAGCCTA
AAGCTTA
– Average frequency 1/1000bp
– SNPs arise as a consequence of mistakes
during normal DNA replication
• Genomic rearrangements
– Duplications, insertions, deletions

Genetics as the basis for variability
in drug response
• Pharmacogenetics
– The effect of genetic variation on drug response.
• Pharmacogenomics
– The application of genomics to the study of human
variability in drug response.
• Pharmacogenetics and pharmacogenomics are

expected to play an important role in the development of
better medicines for populations and targeted therapies
with improved benefit/risk ratios for individuals

Personalized Medicine
The ability to offer
• The Right Drug
• To The Right Patient
• For The Right Disease
• At The Right Time
• With The Right Dosage
Genetic and metabolic data

will allow drugs to be
tailored to patient
subgroups

Benefits of Personalized Medicine
• Better matching patients to drugs instead of “trial and error
• Customized pharmaceuticals may eliminate life-threatening

adverse reactions
• Reduce costs of clinical trials by

– Quickly identifying total failures
– Favourable responses for particular backgrounds
• Improved efficacy of drugs

Personalized Medicine : BiDil
• Combination pill containing two medications for
heart failure, cardiovascular disease, and/or
diabetes.
• Clinical trials did not show overall benefit across
entire population.
• Subgroup of African-descent patients showed
benefit
– BiDil approved for use in African-descent patients.

Pharmacokinetics and pharmacodynamics
are essential to assess the drug efficacy.
• Pharmacokinetics
– What the body does to the drug
– dose, dosage regimen, delivery form
– Drug fate: Absorption, distribution, metabolism, and elimination
of drugs (ADME)
• Pharmacodynamics
– What the drug does to the body
– Biochemical and physiological effects of drugs
– mechanism of drug action
– relationship between drug concentration and effect

Codeine
Metabolism
• 5-10% codeine is metabolized
into morphine by CYP2D6
– 7% of caucasians have a
nonfunctional CYP2D6 variant
– <2% are CYP2D6 ultrarapid
metabolizers which may suffer
from opioid intoxication
• 80% codeine normally
converted to glucuronide,
eliminated by kidney.
• inhibition of CYP3A4 or rapid
metabolic variants of CYP2D6
during renal failure would show
toxicity
Gasche Y et al. Codeine intoxication associated with ultrarapid

CYP2D6 metabolism. NEJM 2004 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Drug-Metabolizing Enzymes
Phase I: modification of functional groups Phase II: conjugation with endogenous substitutents
Most DME have clinically relevant polymorphisms

Those with changes in drug effects are separated from pie.
Pharmacogenomics: Translating Functional Genomics into Rational
Cytochrome P450 Enzymes
• Expressed mainly in liver
• Act on:
– Endogenous substrates
– Xenobiotics including plant and fungal products, pollution,
chemicals
– Drugs (metabolize 50-60%)
• Typical reaction:
– Oxidation
– RH + O2 + NADPH + H+  ROH + H2O + NADP+
• Sequence diversity:
– 18 families
– 43 subfamilies
– ~60 genes
– ~100 allelic variants (isoforms)

Participation of the CYP Enzymes in Metabolism of
Some Clinically Important Drugs
CYP Enzyme Examples of substrates
1A1 Caffeine, Testosterone, R-Warfarin
1A2 Acetaminophen, Caffeine, Phenacetin, R-Warfarin
2A6 17β -Estradiol, Testosterone
2B6 Cyclophosphamide, Erythromycin, Testosterone
2C-family Acetaminophen, Tolbutamide (2C9); Hexobarbital, S-
Warfarin (2C9,19); Phenytoin, Testosterone, R- Warfarin,
Zidovudine (2C8,9,19);
2E1 Acetaminophen, Caffeine, Chlorzoxazone, Halothane
2D6 Acetaminophen, Codeine, Debrisoquine
3A4 Acetaminophen, Caffeine, Carbamazepine, Codeine,
Cortisol, Erythromycin, Cyclophosphamide, S- and R-
Warfarin, Phenytoin, Testosterone, Halothane, Zidovudine
S. Rendic Drug Metab Rev 34: 83-448, 2002 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Factors Influencing Activity and Level of CYP Enzymes
Nutrition
Red indicates enzymes important in drug metabolism
S. Rendic Drug Metab Rev 34: 83-448, 2002 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Pharmacogenetics: number of
genes affects drug potency
Nortryptyline:
Anti-depressant
Weinshilboum, R. N Engl J Med 2003;348:529-537 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Use of probe drugs to determine metabolic
activity due to CYP2D6 variants
Antihypertensive debrisoquin decreases blood pressure

Weinshilboum, R. N Engl J Med 2003;348:529-537 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008
Diagnostics
AmpliChip CYP450: Range

of drug metabolism
phenotypes is observed for
individuals based upon the
cytochrome P-450 genes

Is pharmacogenetics in routine
use? NO
• Science still early. Limited data in public domain.
• Fragmentation of drug markets is not attractive to
drug companies.
• Many variations not clinically significant
• Expensive to test for genotype
• Significantly more challenging to track drug drug
interactions

CYP3A4
• Abundant in liver and intestines and
accounts for nearly 50% of CYP450
enzymes.
• Activity can vary markedly among
members of a population
– Constitutive variability is ~5-fold but
can increase to 400-fold through
induction and inhibition
• Activity affected by other drugs:
– St Johns wort is an inducer, 5mg tablet
grapefruit juice is an inhibitor with juice
– Felodipine is a calcium channel
blocker (calcium antagonist), a drug
used to control hypertension (high
blood pressure)

CYP3A4 mediated Drug-Drug Interaction
PXR: pregnane X receptor; RXR: retinoid X receptor

• Protect against xenobiotics
• Diverse drugs activate through heterodimer complex
• Cause drug-drug interactions
Wilson. PXR, CAR, and drug metabolism. Nat Rev Drug Disc 2002
Quantitative Structure-Activity
Relationship (QSAR)
• find consistent relationship between biological activity
and molecular properties, so that these “rules” can be
used to evaluate the activity of new compounds.
• extract features (hydrophobicity, pK, van der Waals radii,
hydrogen bonding energy, conformation)
• build mathematical relationship f(activity|features)
• automatically assesses the contribution of each feature
• can be used to make predictions on a new molecule

3D QSAR for CYP3A4

3D QSAR for CYP3A4 with known
substrates

Drug Metabolic Fate
What are the potential by-products of a drug?
Going beyond QSAR to de novo predictions
Quantify differences in binding due to natural variation.

nsSNPs in Ligand Sites
of Proteins involved in Disease
• Of 9.7M SNPs, 778 nsSNPs
SNP
were located in the predicted
DNA
binding sites of 484 proteins
611 nsSNPs in 351 disease Gene

causing genes (OMIM)
Protein
over 200 genes not associated Ligand

with disease Binding
Disease
• Molecular Mechanism?
Daniel Oropeza, 2006
Honours Thesis

GTP binding site of S. cerevisiae Homolog 2. The ASP 137 ASN mutation has
been shown to cause a decrease in the affinity for GDP (Jones, B et al . 2003).
This mutation has been associated with Chylomicron retention disease.

Qualitative Functional Inference

Genomic Medicine:
Predictive, personalized, and
pre-emptive

Things to Consider
• Does my doctor know enough about
genomic medicine to be advising me?
– Are there genetic counselors available?
• Will the test only be for this condition?
– What if I am susceptible to another disease?
• Who will know about this?
– Doctors… insurance companies?
• How exactly will the results be kept secure
and in confidence?

How much will this cost?
• More drugs may succeed in clinical trials due to
positive outcome for smaller subset
– Will pharma attempt to recoup costs with a pricier drug?
• Will public health cover the costs of genetic

testing?
– Reduce overall health cost due to fewer ADRs
– Should we determine clinically validated genes or
should we sequence the genome?
• How will my insurance premiums be affected?

Michel Dumontier
michel_dumontier@carleton.ca
http://dumontierlab.com

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Towards

Michel Dumontier, Ph.D.

Ottawa Institute for Systems Biology

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• ADR is one of the leading causes of hospitalization and death

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Lipitor blocks the

• May reduce risk of

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Treatment for Acute Pain

increased risk of heart attack and stroke

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

PhRMA Annual Report 2005-2006 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Quality of pharmaceutical innovation varies

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

0% 2% 4% 6% 8% 10% 12% 14% 16%

Source: Fortune Magazine, April 14, 2003

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Determined key residues,

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Matrix Metallo Proteinase Inhibitors (MMPI) are

Melissa Passino. Structural Bioinformatics in Drug Discovery.

Whittaker et al. Chem. Rev. 1999, 99, 2735-2776

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• But poor oral

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Parallel synthetic approach

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Speeds up key steps in drug

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

oral anti- anti-

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Sir William Osler, 1892

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Pharmacogenetics and pharmacogenomics are

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Genetic and metabolic data

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

• Customized pharmaceuticals may eliminate life-threatening

• Reduce costs of clinical trials by

• Improved efficacy of drugs

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Gasche Y et al. Codeine intoxication associated with ultrarapid

Most DME have clinically relevant polymorphisms

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Weinshilboum, R. N Engl J Med 2003;348:529-537 Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Antihypertensive debrisoquin decreases blood pressure

AmpliChip CYP450: Range

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008

Dumontier::BIOL4301:Towards Personalized Medicine:Nov 25, 2008