Drug discovery and development involves several basic steps: choosing a disease target and drug target, identifying a lead compound, optimizing the lead compound's structure through structure-activity relationships, determining toxicity and efficacy in animal models, and carrying out clinical trials in humans. Key parts of the process include identifying the pharmacophore of active compounds, improving pharmacokinetic properties like absorption and metabolism, ensuring safety through toxicity testing, and developing an efficient manufacturing process. Thalidomide highlights the importance of thorough safety testing, as its approval without adequate pregnancy testing led to severe birth defects in thousands of children.

1. Drug Discovery and
Development
How are drugs discovered and
developed?

2. Basic Steps
• Choose a disease
• Choose a drug target
• Identify a “bioassay”
bioassay = A test used to determine biological
activity.
• Find a “lead compound”
“lead compound” = structure that has some activity
against the chosen target, but not yet good
enough to be the drug itself.
• If not known, determine the structure of the “lead
compound”
• Synthesize analogs of the lead
• Identify Structure-Activity-Relationships (SAR’s)

3. • Structure-Activity-Relationship (SAR) = How does
the activity change as structure is systematically
altered?
• Identify the “pharmacophore”
pharmacophore = the structural features directly
responsible for activity
• Optimize structure to improve interactions with
target
• Determine toxicity and efficacy in animal models.
• Determine pharmacodynamics and
pharmacokinetics of the drug.
• Pharmacodynamics explores what a drug does to
the body, whereas pharmacokinetics explores
what the body does to the drug.

4. Basic steps (cont.)
• Patent the drug
• Study drug metabolism
• Test for toxicity
• Design a manufacturing process
• Carry out clinical trials
• Market the drug

5. 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)

6. Choosing a
Disease
• 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)

7. Choosing a Disease (cont.)
• Most research is
carried out on diseases
which afflict “first world”
countries: (e.g. cancer,
cardiovascular
diseases, depression,
diabetes, flu, migraine,
obesity).

8. 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.

9. Identifying a Drug Target
• Drug Target = specific macromolecule,
or biological system, which the drug will
interact with
• Sometimes this can happen through
incidental observation…

10. Identifying a Drug Target (cont.)
•Example: In addition to their being able to inhibit the uptake
of noradrenaline, the older tricyclic antidepressants were
observed to “incidentally” inhibit serotonin uptake. Thus, it was
decided to prepare molecules which could specifically inhibit
serotonin uptake. It wasn’t clear that this would work, but it
eventually resulted in the production of fluoxetine (Prozac).
NH2
N
H
HO
serotonin
O
HN
prozac
N
N CH3
H3C
Imipramine
(a classical tricyclic antidepressant)
F3C

11. The mapping of the human
genome should help!
• In the past, many medicines (and lead
compounds) were isolated from plant sources.
• Since plants did not evolve with human beings in
mind, the fact that they posses chemicals which
results in effects on humans is incidental.

12. • Having the genetic code for the production of an
enzyme or a receptor may enable us to over-
express that protein and determine its structure
and biological function. If it is deemed important
to the disease process, inhibitors (of enzymes), or
antagonists or agonists of the receptors can be
prepared through a process called rational drug
design.

13. Simultaneously, Chemistry is Improving!
• This is necessary, since,
ultimately, plants and natural
sources are not likely to
provide the cures to all
diseases.
• In a process called
“combinatorial chemistry”
large numbers of compounds
can be prepared at one time.
• The efficiency of synthetic
chemical transformations is
improving.

14. Selectivity is Important!
• e.g. targeting a bacterial enzyme, which
is not present in mammals, or which
has significant structural differences
from the corresponding enzyme in
mammals

15. The Standards are Being Raised
• More is known about the biological
chemistry of living systems
• For example: Targeting one subtype of
receptor may enable the pharmaceutical
chemist to avoid potentially troublesome
side effects.

16. Problems can
arise
• Example: The chosen target, may over time,
lose its sensitivity to the drug
• Example: The penicillin-binding-protein (PBP)
known to the the primary target of penicillin in the
bacterial species Staphylococcus aureus has
evolved a mutant form that no longer recognizes
penicillin.

17. Choosing the Bioassay
• Definitions:
– In vitro: In an artificial environment, as in a test
tube or culture media
– In vivo: In the living body, referring to tests
conductedin living animals
– Ex vivo: Usually refers to doing the test on a
tissue taken from a living organism.

18. Choosing the Bioassay (cont.)
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

19. Choosing the Bioassay (cont.)
In vivo tests
• More expensive
• May cause suffering to animals
• Results may be clouded by interference
with other biological systems

20. Finding the Lead
Screening Natural Products
• Plants, microbes, the marine world, and
animals, all provide a rich source of
structurally complex natural products.

21. • It is necessary to have a quick assay for
the desired biological activity and to be
able to separate the bioactive
compound from the other inactive
substances
• Lastly, a structural determination will
need to be made

22. Finding the Lead (cont.)
Screening synthetic banks
• Pharmaceutical companies have
prepared thousands of compounds
• These are stored (in the freezer!),
cataloged and screened on new targets
as these new targets are identified

23. Finding the Lead (cont.)
Using Someone Else’s Lead
• Design structure which is similar to existing lead, but
different enough to avoid patent restrictions.
• Sometimes this can lead to dramatic improvements
in biological activity and pharmacokinetic profile.
(e.g. modern penicillins are much better drugs than
original discovery).

24. Finding the Lead (cont.)
Enhance a side effect
O
NH
S
O
O
NH
tolbutamide
NH2S
O
O
H2N
sulphanilamide
(an antibacterial with the side effect of
lowering glucose levels in the blood and also
diuretic activity)
(a compound which has been optimized to only
lower blood glucose levels. Useful in the treatment
of Type II diabetes.)
S
NH
N
O O
S
O
OH2N
Cl
Chlorothiazide
(a compound which has been optimized to only display diuretic
activity.)

25. Use structural similarity to a natural ligand
N
NH2
HO
H
N
N(CH3)2
H
S
H
N
O O
H3C
5-Hydroxytryptamine (5-HT)
Serotonin (a natural neurotransmitter
synthesized in certain neurons in the CNS)
Sumatriptan (Imitrex)
Used to treat migrain headaches
known to be a 5-HT1 agonist

26. Finding the Lead (cont.)
Computer-Assisted Drug Design
• If one knows the precise molecular structure of
the target (enzyme or receptor), then one can
use a computer to design a perfectly-fitting
ligand.
• Drawbacks: 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).
Thus, most programs are somewhat inaccurate
representations of reality.

27. Finding a Lead (cont.)
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
• Example: development of Viagra to treat
erectile dysfunction

28. Finding a Lead (cont.)
Sildenafil (compound UK-92,480) was synthesized by a
group of pharmaceutical chemists working at Pfizer's
Sandwich, Kent research facility in England.
It was initially studied for use in hypertension (high blood
pressure) and angina pectoris (a form of ischaemic
cardiovascular disease).
Phase I clinical trials under the direction of Ian Osterloh
suggested that the drug had little effect on angina, but that
it could induce marked penile erections.

29. 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 on March 27,
1998, 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.

30. Finding a Lead (cont.)
N
N
S
O
O
N
N
N
NH
O
O
viagra
(Sildenafil)

32. 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”)

34. The pharmacophore is the precise section of the
molecule that is responsible for biological activity

35. • This may enable one to prepare a more active molecule
• This may 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: R-OH can be converted to R-OCH3 to see if O-H is
involved in an important interaction
• Example: R-NH2 can be converted to R-NH-COR’ to see if
interaction with positive charge on protonated amine is an
important interaction

36. Link
Link

37. Next step: Improve
Pharmacokinetic Properties
• Improve pharmacokinetic properties.
pharmacokinetic = The study of absorption,
distribution, metabolism and excretion of a
drug (ADME).
• Video
• exercise=MedicationDistribution&title=Medica
tion%20Absorption,%20Distribution,
%20Metabolism%20and%20Excretion
%20Animation&publication_ID=2450

38. 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.

39. Metabolism of Drugs (cont.)
• Phase 1 Metabolism involves the
conversion of nonpolar bonds (eg C-H
bonds) to more polar bonds (eg C-OH
bonds).
• A key enzyme is the cytochrome P450
system, which catalyzes this reaction:
RH + O2 + 2H+
+ 2e–
ROH + H→ 2O

40. Mechanism of Cytochrome
P450

41. Phase I metabolism may
either detoxify or toxify.
• 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

43. The Liver
• Oral administration frequently brings the
drugs (via the portal system) to the liver

44. Metabolism of Drugs (cont.)
• Phase II metabolism links the drug to still
more polar molecules to render them even
more easy to excrete
O O
OHHO
OH
HO
O P
HO
O
O
P
HO O
O O
HO
OH
N
NH
O
O
R OH
O O
OHHO
OH
HO
O
R
Glucuronic Acid
UDP Glucuronic Acid
More easily excreted than ROH itself
glucuronosyltransferase
enzyme
Drug
Drug

45. Metabolism of Drugs (cont.)
• Another Phase II reaction is sulfation
(shown below)
R OH
O N
N
N
N
NH2
OHO
OP
O
O-
OS
O
O
O-
PO O-
O-
3'-Phosphoadenosine-5'-phosphosulfate
Drug
R O
SO3
-
Sulfated Drug
(more easily excreted)

46. Phase II Metabolism
• Phase II reactions most commonly
detoxify
• Phase II reactions usually occur at polar
sites, like COOH, OH, etc.

47. Manufacture of Drugs
• Pharmaceutical companies must make a profit to continue to exist
• Therefore, drugs must be sold at a profit
• One must have readily available, inexpensive starting materials
• One must have an efficient synthetic route to the compound
– As few steps as possible
– Inexpensive reagents

48. • The route must be suitable to the
“scale up” needed for the production of
at least tens of kilograms of final
product
• This may limit the structural complexity
and/or ultimate size (i.e. mw) of the
final product
• In some cases, it may be 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.

49. 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

50. Example: 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.
Antiemetic = a medication that helps prevent
and control nausea and vomiting

52. Birth defects
caused by use of thalidomide

53. Example: 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.
N
O
O
NH
O
O
Thalidomide
Phocomelia presents at birth very short or absent long bones
and flipper-like appearance of hands and sometimes feet.

54. Example: Thalidomide
•Researchers, however, continued to work with the drug. Soon
after its banishment, 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.
Teratogenic = Causing malformations in a fetus

55. 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 it is now approved by the FDA for use in this
malignancy. There are studies underway to determine the drug's
effects on arachnoiditis, Crohn's disease, and several types of
cancers.

56. Clinical Trials
• Phase I: Drug is tested on healthy volunteers
to determine toxicity relative to dose and to
screen for unexpected side effects

57. Clinical Trials
• 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.

58. Clinical Trials
• Phase III: Drug is tested on much larger
group of patients and compared with existing
treatments and with a placebo

59. Clinical Trials
• Phase IV: Drug is placed on the market and patients
are monitored for side effects