Drug Discovery

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Drug Discovery
Average time to bring drug to market 12-15
yrs Average cost 600-900 million For every
20000 compounds evaluated in animals 10 make
it to human clinical trials 1 goes to market
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DRUG DESIGN AND DEVELOPMENT
Stages
1) Identify target disease 2) Identify drug
target 3) Establish testing procedures 4) Find
a lead compound 5) Structure Activity
Relationships (SAR) 6) Identify a pharmacophore
7) Drug design- optimising target interactions
8) Drug design - optimising pharmacokinetic
properties 9) Toxicological and safety tests 10)
Chemical development and production 11) Patenting
and regulatory affairs 12) Clinical trials
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1. TARGET DISEASE

• Priority for the Pharmaceutical Industry
• Can the profits from marketing a new drug
  outweigh the cost of developing and testing that
  drug
• Questions to be addressed
• Is the disease widespread
• (e.g. cardiovascular disease ulcers malaria)
• Does the disease affect the first world
• (e.g. cardiovascular disease ulcers)
• Are there drugs already on the market
• If so what are there advantages and
  disadvantages
• (e.g. side effects)
• Can one identify a market advantage for a new
  therapy

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2. DRUG TARGETS
A) LIPIDS Cell Membrane Lipids B) PROTEINS
Receptors Enzymes Carrier
Proteins Structural Proteins (tubulin) C)
NUCLEIC ACIDS DNA RNA D)
CARBOHYDRATES Cell surface carbohydrates An
tigens and recognition molecules
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2. DRUG TARGETS
TARGET SELECTIVITY

• Between species
• Antibacterial and antiviral agents
• Identify targets which are unique to the invading
  pathogen
• Identify targets which are shared but which are
  significantly different in structure
• Within the body
• Selectivity between different enzymes receptors
  etc.
• Selectivity between receptor types and subtypes
• Selectivity between isozymes
• Organ selectivity

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3. TESTING DRUGS

• Tests are required in order to find lead
  compounds and for drug optimisation
• Tests can be in vivo or in vitro
• A combination of tests is often used in research
  programs

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3.2 in vitro Tests

• Tests not carried out on animals/humans
• Target molecules (e.g. isolated enzymes or
  receptors) Cells (e.g. cloned
  cells) Tissues (e.g. muscle
  tissue) Organs Micro-organisms (for
  antibacterial agents)
• More suitable for routine testing
• Used in high throughput screening
• Measure the interaction of a drug with the target
  but not the ability of the drug to reach the
  target
• Results are easier to rationalise - less factors
  involved
• Does not demonstrate a physiological or clinical
  effect
• Does not identify possible side effects

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3.1 in vivo Tests

• Carried out on live animals or humans
• Measure an observed physiological effect
• Measure a drugs ability to interact with its
  target and its ability to reach that target
• Can identify possible side effects
• Rationalisation may be difficult due to the
  number of factors involved
• Transgenic animals - genetically modified animals
  
• Drug potency - concentration of drug required to
  produce 50 of the maximum possible effect
• Therapeutic ratio/index - compares the dose level
  of a drug required to produce a desired effect in
  50 of the test sample (ED50) versus the dose
  level that is lethal to 50 of the sample (LD50)

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3.2.1 Enzyme Inhibition Tests

• Identify competitive or non competitive
  inhibition
• Strength of inhibition measured as IC50
• IC50 concentration of inhibitor required to
  reduce enzyme activity by 50

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3.2.2 Testing with Receptors

• Not easy to isolate membrane bound receptors
• Carried out on whole cells tissue cultures or
  isolated organs
• Affinity - strength with which compounds bind to
  a receptor
• Efficacy - measure of maximum biochemical effect
  resulting from binding of a compound to a
  receptor.
• Potency - concentration of an agonist required to
  produce 50 of the maximum possible effect.

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Drug Discovery
Drugs generally are not discovered directly
Lead compound
has desired activity plus undesirable
characteristics toxicity other
activities insolubility metabolism problems
oral bioavailability
Lead modified by synthesis
Produces a drug candidate
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4 The Lead Compound
Introduction

• A compound demonstrating a property likely to be
  therapeutically useful
• The level of activity and target selectivity are
  not crucial
• Used as the starting point for drug design and
  development
• Found by design (molecular modelling or NMR) or
  by screening compounds (natural or synthetic)
• Need to identify a suitable test in order to find
  a lead compound
• Active Principle - a compound that is isolated
  from a natural extract and which is principally
  responsible for the extracts pharmacological
  activity. Often used as a lead compound.

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Medicinal Chemistry Folklore
Earliest medicines 5100 years ago
China Chang Shan - contains alkaloids used
today in the treatment of malaria and for
fevers Ma Huang - contains ephedrine used as a
heart stimulant and for asthma. Now used by body
builders and endurance athletes because it
quickly converts fat into energy and increases
strength of muscle fibers. Modern
therapeutics Extract of foxglove plant cited by
Welsh physicians in 1250. Used to treat
congestive heart failure in 1785.
Contains digitoxin and digoxin today called
digitalis
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Discovery of New Drugs
Nature is still an excellent source of new drugs
(or precursors of new drugs). Of the 20 leading
drugs in 1999 9 were derived from natural
products. From 1983-1994 almost 40 of the 520
new drugs approved were natural products or
derived from natural products. 60 of anti-tumor
and anti-infective drugs are natural products or
derived from natural products.
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4.1 Sources of Lead Compounds
A) The Natural World
B) The Synthetic World
C) The Virtual World
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Drug Discovery Without a Lead
Penicillins 1928 - Fleming
Bacteria lysed by green mold

• 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

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Structure of penicillin elucidated in 1944 -
X-ray crystal structure by Dorothy Hodgkin
(Oxford)
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4.3 Lead Compounds from the Natural World
PLANT EXTRACTS

• OPIUM - Morphine

• CINCHONA BARK - Quinine

• YEW TREE - Taxol

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4.3 Lead Compounds from the Natural World
PLANT EXTRACTS
WILLOW TREE - SALICYLIC ACID
Aspirin
COCA BUSH - COCAINE
Procaine
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4.3 Lead Compounds from the Natural World
PLANTS AND ANCIENT RECORDS
ARTEMISININ
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4.3 Lead Compounds from the Natural World
VENOMS AND TOXINS
Teprotide
Captopril (anti-hypertensive)
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4.3 Lead Compounds from the Natural World
VENOMS AND TOXINS
Tubocurarine (from curare)
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4.3 Lead Compounds from the Natural World
VENOMS AND TOXINS
Tubocurarine (from curare)
Atracurium (Neuromuscular blocker)
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4.3 Lead Compounds from the Natural World
ENDOGENOUS COMPOUNDS
NATURAL LIGANDS FOR RECEPTORS
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4.3 Lead Compounds from the Natural World
ENDOGENOUS COMPOUNDS
NATURAL LIGANDS FOR RECEPTORS
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4.3 Lead Compounds from the Natural World
ENDOGENOUS COMPOUNDS
NATURAL SUBSTRATES FOR ENZYMES
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4.4 Lead Compounds from the Synthetic World
SULFANILAMIDE
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4.4 Lead Compounds from the Synthetic World
RUBBER INDUSTRY
ANTABUSE
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - PEPTIDE SYNTHESIS
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - HETEROCYCLIC SYNTHESIS
RESIN BEAD
N
N
O
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - HETEROCYCLIC SYNTHESIS
N
N
O
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - HETEROCYCLIC SYNTHESIS
N
N
O
EtO
O
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - HETEROCYCLIC SYNTHESIS
N
N
N
HN
O
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4.4 Lead Compounds from the Synthetic World
COMBINATORIAL SYNTHESIS - HETEROCYCLIC SYNTHESIS
RESIN BEAD
N
N
N
HN
O
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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 100000 compounds a day
1990 200000 compounds screened per
year 1995 5-6 106 compounds screened per
year 2000 gt 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.
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Lead Discovery Approaches
1. 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
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Lead Discovery Approaches (contd)
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
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4.5 Lead Compounds - Impact of the human genome
project
The Past
Lead Compound
The Future
Targets
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Problems with Rational Approaches
Cannot predict toxicity/side effects. Cannot
predict transport/distribution. Cannot predict
metabolic fate.
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4.7 Design of Lead Compounds using NMR
Spectroscopy
Binding Site
Protein
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4.7 Design of Lead Compounds using NMR
Spectroscopy
Protein
NO OBSERVABLE BIOLOGICAL EFFECT
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4.7 Design of Lead Compounds using NMR
Spectroscopy
13C NMR
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4.7 Design of Lead Compounds using NMR
Spectroscopy
CH3
CH
CH
CH3
CH2
CH2
CH
C
C
13C NMR
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4.7 Design of Lead Compounds using NMR
Spectroscopy
Protein
Optimise epitope
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4.7 Design of Lead Compounds using NMR
Spectroscopy
Protein
Optimise epitope
Optimise epitope
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4.7 Design of Lead Compounds using NMR
Spectroscopy
Link
Protein
Optimise epitope
Optimise epitope
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4.7 Design of Lead Compounds using NMR
Spectroscopy
LEAD COMPOUND
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Example of SAR by NMR
Inhibition of stromelysin a matrix
metalloprotease (degrades extracellular matrix
components in tissue remodeling and in arthritis
osteoporosis and cancer)
Site 2
Linker
Site 1
Kd 17nM
Kd 20M
Kd 17mM
Took 6 months to identify 2.60. Prior to this no
leads had been identified.