Drug Discovery and

Development
 Choosing a Disease
• Pharmaceutical companies are commercial enterprises
• Pharmaceutical companies will, therefore, tend to avoid products with a
small market (i.e. a disease which only affects a small subset of the
population)
• Pharmaceutical companies will also avoid products that would be
consumed by individuals of lower economic status (i.e. a disease which
only affects third world countries)
• Most research is carried out on diseases which afflict “first world”
countries: (e.g. cancer, cardiovascular diseases, depression, diabetes,
flu, migraine, obesity).
 The Orphan Drug Act
• The Orphan Drug Act of 1983 was passed to encourage pharmaceutical
companies to develop drugs to treat diseases which affect fewer than
200,000 people in the US
• Under this law, companies who develop such a drug are entitled to market it
without competition for seven years.
• This is considered a significant benefit, since the standards for patent
protection are much more stringent.
 Identifying a Drug Target
Drug Target = specific macromolecule, or biological system,
which the drug will interact with
Through incidental observation
•Tricyclic antidepressants inhibit the uptake of noradrenaline,
•They “incidentally” inhibit serotonin uptake as well.
•Molecules are prepared which could specifically inhibit
serotonin uptake and eventually resulted in the production of
fluoxetine (Prozac).

HO

N NH2
F3C
HN

CH3 O
N N
H
H3C
serotonin prozac

Imipramine
(a classical tricyclic antidepressant)
 Choosing the Bioassay
– In vitro: In an artificial environment, as in a test
tube or culture media
– In vivo: In the living body, referring to tests
conducted in living animals
– Ex vivo: Usually refers to doing the test on a
tissue taken from a living organism.
 In vitro testing
• Has advantages in terms of speed and requires
relatively small amounts of compound
• Speed may be increased to the point where it is
possible to analyze several hundred compounds in a
single day (high throughput screening)
• Results may not translate to living animals

In vivo tests
• More expensive
• May cause suffering to animals
• Results may be clouded by interference with
other biological systems
 Lead Compound
It is a chemical compound obtained from natural or
synthetic sources that possesses a particular biological
activity.
A lead can be characterized as a compound that has
some desirable biological activity, not extremely polar
or lipophilic, and not contain toxic or reactive
functional groups.
Often, molecular weight (< 350) and lipophilicity (log P < 3)
are considered the essential characteristics of a drug-like
lead.
The lead should also have a series of congeners that
modulate biological activity, indicating that further structural
modification will improve selectivity and potency.
7
Drug design = exploration of the lead compounds
•The search for a new lead
•The exploitation of the existing
leads to produce
more active compounds with less toxicity than the
original lead compound.
Example:
i. Sulphanilamide- isolated from the degradation of
prontosil or synthesized chemically and acts as
antibacterial agent.
ii. Lead compound from natural sources: Morphine
from opium, cocaine from coca leaves, and quinine
from the bark of cinchona tree.
8
 Examples of Natural Products as Leads & Drugs
Cardiac glycosides, morphine, quinine, salicylic acid, taxol, camptothecin,
penicillin, cyclosporin A, warfarin, artemisine….
O
OH OH
HO OMe
HO
N H H H OH
N
HO
O H H H H O O
O
HO HO
O O OMe
RO 17-ethynylestradiol norethindrone
R = H: Morphine O OH
R = Me: Codeine (the "Pill"; contraceptive)
(pain killer) Clarithromycin
(antibacterial)

CO2H
HO O CO2H
O N O
N OH
O
S O 3
H H O OH N N
NH2 N 11 N 4
10 1 N 2
N O H O O
Ampicillin Clavulanic acid
-lactamase inhibitor) O O HN
(antibiotic) O
9 H 7
5
8 N 6 N O
N N
H
O O
Augmentin 9
(antibiotic) Cyclosporine A
 Finding the Lead
Screening Natural Products
• Plants, microbes, the marine world, and animals
provide a rich source of structurally complex natural
products.
• A quick assay for the desired biological activity has to
be developed to separate the bioactive compound from
the other inactive substances
• A structure of the lead has to be known
• Pharmaceutical companies have prepared thousands
of compounds, stored (in the freezer), cataloged and
screened on new targets.
 Finding the Lead
Design structure which is similar to existing lead, but
different enough to avoid patent restrictions.
Sometimes dramatic improvements in biological activity
and pharmacokinetic profile leadsOO
to a drug. (e.g. modern
penicillins are much better
HHNN drugsSSthan
NH original discovery).
NH 2
2
2
2

OO
sulphanilamide
O
sulphanilamide
2(an
H(an antibacterialwith
Nantibacterial withthe
the side
S side
NH effect
2 ofof
effect
loweringglucose
lowering glucoselevels
levelsininthe
theblood
bloodand
andalso
also
diuretic activity)
diuretic activity) O
sulphanilamide
(an antibacterial with the side effect of
lowering glucose levels in the blood and also
diuretic activity)

ClCl NN
OO
OO SS OO NH
OO SS
NH
NH
NH H N SS
NH
HCl
2N
2
OO OO OO
N
NH
O Chlorothiazide
tolbutamide
O S
tolbutamide O Chlorothiazide
O NH
(a(acompound
compoundwhich
whichhashasbeen
beenoptimized
NH optimized totoonly
only (a(acompound
compoundwhich
Swhichhas
hasbeen
beenoptimized
optimized
S totoonly
onlydisplay
displaydiuretic
diuretic
lower blood glucose levels. Useful in the treatment
lower blood glucose levels. Useful in the treatment activity.)
H
activity.) 2 N O O
ofofType
TypeIIIIdiabetes.)
diabetes.)
NH O
 Finding the Lead
Structural Similarity to a Natural Ligand

NH2 NH2 N(CH3)2

H H
HO N N
H3C S H3C S
O O O O
N N N N
H H H H
-Hydroxytryptamine (5-HT) Sumatriptan (Imitrex)
5-Hydroxytryptamine
otonin (a natural neurotransmitter (5-HT) Sumatriptan (Imitrex)
Used to treat migrain headaches
sized inSerotonin (a natural
certain neurons in theneurotransmitter
CNS) Used to treat migrain headac
known to be a 5-HT1 agonist
synthesized in certain neurons in the CNS) known to be a 5-HT1 agoni
 Finding the Lead

Computer-Assisted Drug Design

• If the precise molecular structure of the target (enzyme or
receptor) is known, then computer can be used to design
a perfectly-fitting ligand.
• But, most commercially available programs do not allow
conformational movement in the target (as the ligand is
being designed and/or docked into the active site.
 Finding the Lead
Drug discovery by serendipity
• The use of nitrous oxide and ether as narcotic gases in
surgery resulted from the observation that people who
inhaled these chemicals did not experience any pain after
injury.

• The vasodilatory activity of amyl nitrite and nitroglycerin

was discovered by chemists who developed strong
headaches after inhaling or ingesting minor amounts.

• A wrong working hypothesis on chloral hydrate (which was

supposed to degrade metabolically to narcotic chloroform)
led to its application as a strong sedative (in reality, the
metabolite trichloroethanol is the active form). Similarly,
urethane was supposed to release ethanol but is a hypnotic
by itself.
14
15
 Serendipity: a chance occurrence

Must be accompanied by an experimentalist who

understands the “big picture” (and is not solely
focused on his/her immediate research goal), who
has an open mind toward unexpected results, and
who has the ability to use deductive logic in the
explanation of such results.
Example:
•Penicillin discovery
•Development of Viagra to treat erectile dysfunction
 Finding a Lead (cont.)

Sildenafil (compound UK-92,480) was

synthesized by a group of
pharmaceutical chemists working at
O
Pfizer's Sandwich, Kent research N
N

facility in England. N

It was initially studied for use in NH

O
O S
hypertension and angina pectoris. O
N

Phase I clinical trials under the

direction of Ian Osterloh suggested N

that the drug had little effect on viagra

angina, but that it could induce (Sildenafil)

marked penile erections.

Pfizer therefore decided to market it for erectile dysfunction,
rather than for angina.
The drug was patented in 1996, approved for use in erectile
dysfunction by the Food and Drug Administration in1998,
becoming the first pill approved to treat erectile dysfunction
in the United States, and offered for sale in the United
States later that year.
It soon became a great success: annual sales of Viagra in
the period 1999–2001 exceeded $1 billion.
 Structure-Activity-Relationships (SAR’s)
Once a lead has been discovered, it is important to understand
precisely which structural features are responsible for its
biological activity (i.e. to identify the “pharmacophore”)
The pharmacophore is the precise section of the molecule that
is responsible for biological activity
• Enable one to prepare a more active molecule
• Allow the elimination of “excessive” functionality, thus reducing
the toxicity and cost of production of the active material
• This can be done through synthetic modifications
• Example:
1. R-OH can be converted to R-OCH3 to see if O-H is involved in
an important interaction
2. R-NH2 can be converted to R-NH-COR’ to see if interaction with
positive charge on protonated amine is an important interaction
 Improve Pharmacokinetic Properties
Pharmacokinetic = The study of absorption, distribution,
metabolism and excretion of a drug (ADME).

Metabolism of Drugs
• The body regards drugs as foreign substances, not produced
naturally.
• Sometimes such substances are referred to as “xenobiotics”
• Body has “goal” of removing such xenobiotics from system
by excretion in the urine
• The kidney is set up to allow polar substances to escape in
the urine, so the body tries to chemically transform the drugs
into more polar structures.
 Metabolism of Drugs
• Phase 1 Metabolism involves the conversion of nonpolar
bonds (eg C-H bonds) to more polar bonds (e.g. C-OH bonds).
• A key enzyme is the cytochrome P450 system, which catalyzes
this reaction:
RH + O2 + 2H+ + 2e– → ROH + H2O
• Phase I reactions produce a more polar molecule that is easier
to eliminate.
• Phase I reactions can sometimes result in a substance more
toxic than the originally ingested substance.
• An example is the Phase I metabolism of acetonitrile
• Phase I metabolism may either detoxify or toxify.
 Metabolism of Drugs
• Phase II metabolism links the drug to still more polar
molecules to render them even more easy to excrete
UDP Glucuronic Acid

Glucuronic Acid
HO O
O
P O
HO O
O P O O O
NH
glucuronosyltransferase O O
Drug
O O N enzyme HO R
HO HO O

OH HO OH
HO OH
OH
OH

More easily excreted than ROH itself

R OH

Drug
 Metabolism of Drugs
• Another Phase II reaction is sulfation (shown below)
NH2

N
O O N

O S O P O
O N
O-
N SO3-
R OH
O-
R O
Drug
Sulfated Drug
O OH (more easily excreted)
O P O-

O-

3'-Phosphoadenosine-5'-phosphosulfate

• Phase II reactions most commonly detoxify

• Phase II reactions usually occur at polar sites, like COOH,
OH, etc.
 Manufacture of Drugs
• Readily available, inexpensive starting materials
• Efficient synthetic route to the compound
– As few steps as possible
– Inexpensive reagents
• Suitability of the route to “scale up” for the production of at
least tens of kilograms of final product
• The structural complexity and/or ultimate size (i.e. mw) of the
final product
• Sometimes it is useful to design microbial processes which
produce highly functional, advanced intermediates. This type
of process usually is more efficient than trying to prepare the
same intermediate using synthetic methodology.
 Toxicity
• Toxicity standards are continually becoming tougher
• Must use in vivo (i.e. animal) testing to screen for
toxicity
– Each animal is slightly different, with different metabolic
systems, etc.
– Thus a drug may be toxic to one species and not to another
 Thalidomide
Thalidomide was developed by German pharmaceutical company Grünenthal.

It was sold from 1957 to 1961 in almost 50 countries under at least 40 names.

Thalidomide was chiefly sold and prescribed during the late 1950s and early 1960s to
pregnant women, as an antiemetic to combat morning sickness and as an aid to help
them sleep.

Before its release, inadequate tests were performed to assess the drug's safety, with
catastrophic results for the children of women who had taken thalidomide during their
pregnancies.
 Thalidomide
From 1956 to 1962, approximately 10,000 children were born
with severe malformities, including phocomelia, because their
mothers had taken thalidomide during pregnancy.
In 1962, in reaction to the tragedy, the United States Congress
enacted laws requiring tests for safety during pregnancy before
a drug can receive approval for sale in the U.S.
O

N O

NH

O O

Thalidomide

Phocomelia presents at birth very short or absent long bones

and flipper-like appearance of hands and sometimes feet.
 Thalidomide
Researchers, an Israeli doctor discovered anti-inflammatory
effects of thalidomide and began to look for uses of the
medication despite its teratogenic effects.
He found that patients with erythema nodosum leprosum, a
painful skin condition associated with leprosy, experienced
relief of their pain by taking thalidomide.
Further work conducted in 1991 by Dr. Gilla Kaplan at
Rockefeller University in New York City showed that
thalidomide worked in leprosy by inhibiting tumor necrosis
factor alpha. Kaplan partnered with Celgene Corporation to
further develop the potential for thalidomide.
Subsequent research has shown that it is effective in multiple
myeloma and approved by the FDA for use in this malignancy.
(Studies underway to determine the drug's effects on
arachnoiditis, Crohn's disease, and several types of cancers)
 Clinical Trials
• Phase I: Drug is tested on healthy volunteers to
determine toxicity relative to dose and to screen for
unexpected side effects
• Phase II:Drug is tested on small group of patients to
see if drug has any beneficial effect and to
determine the dose level needed for this effect.
• Phase III: Drug is tested on much larger group of
patients and compared with existing treatments and
with a placebo
• Phase IV: Drug is placed on the market and patients
are monitored for side effects
Clinical development – “Linking bench to bedside”

Phase I studies 20 to 30 healthy volunteers

Investigate: - Safety and tolerability

- Pharmacokinetics
- Pharmacodynamics
Example: Dose titration - first application in humans

toxic
Dosage

therapeutic
(mg)

subtherapeutic

Treatment groups
Clinical development – “Linking bench to bedside” (continued)

Phase II studies 100 to 500 patient volunteers

Investigate: - Safety and tolerability

- Pharmacokinetics
- Pharmacodynamics
- Efficiency
- Dosage to effect relationship

Study design: - Dosage comparison

Antitumor drugs: Combination of Phase I and II at an early stage of drug

development is possible.
 Overall aim of Phase III: Risk-benefit evaluation

Phase III studies are “pivotal studies” = outcome is crucial for the
decision taking of the regulatory authorities.