The document outlines the multi-step process of drug discovery and development. Key steps include: 1) Choosing a disease target and drug target. Common targets are diseases in developed countries. 2) Identifying a "lead compound" with some bioactivity against the target through screening natural products, synthetic libraries, or modifying existing drugs. 3) Optimizing the lead through structure-activity relationship studies and analog synthesis to improve potency and selectivity and identify the pharmacophore responsible for activity. 4) Testing analogs in animal and human clinical trials to determine toxicity, efficacy, and pharmacokinetics before patenting and commercialization. The process aims to continually improve drug properties while avoiding side effects.

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

2. • Choose a disease
• Choose a drug target
• Identify a “bioassay”
bioassay = A test used to determine biological
activity.

3. • 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”

4. •
•
•
•
Synthesize analogs of the lead
Identify Structure-Activity-Relationships (SAR’s)
Synthesize analogs of the lead
Identify Structure-Activity-Relationships (SAR’s)

5. • Identify the “pharmacophore”
pharmacophore = the structural features directly
responsible for activity
• Optimize structure to improve interactions with
target

6. • Determine toxicity and efficacy in
animal models.

7. • 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.

8. • Patent the drug
• Continue to study drug metabolism
• Continue to test for toxicity

9. • Design a manufacturing process
• Carry out clinical trials
• Market the drug

10. 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)

11. 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)

12. 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).

13. 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

14. • 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.

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

16. 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).
HO
NH2
N
N
CH3
H3C
Imipramine
(a classical tricyclic antidepressant)
N
H
serotonin
F3C
HN
O
prozac

17. 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.

18. • Having the genetic code for the production of an
enzyme or a receptor may enable us to overexpress 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.

19. 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.

20. 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

21. 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.

22. 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.

23. 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.

24. 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

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

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

27. • 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

28. 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

29. 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).

30. Finding the Lead (cont.)
Enhance a side effect
O
H2N
S
NH2
O
sulphanilamide
(an antibacterial with the side effect of
lowering glucose levels in the blood and also
diuretic activity)
N
Cl
O
O
S
NH
O
NH
tolbutamide
(a compound which has been optimized to only
lower blood glucose levels. Useful in the treatment
of Type II diabetes.)
O
H2N
NH
S
S
O
O
O
Chlorothiazide
(a compound which has been optimized to only display diuretic
activity.)

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

32. 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.

33. 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

34. 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.

35. 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.

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

38. 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”)

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

41. •
•
•
•
•
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

42. Link

43. 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

44. 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.

45. 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 + H2O

46. Mechanism of Cytochrome
P450

47. 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

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

51. Metabolism of Drugs (cont.)
• 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
HO
O
O
P
O
P
O
O
O
NH
O
glucuronosyltransferase
enzyme
N
HO
OH
OH
O
Drug
O
HO
R
O
HO
HO
O
O
HO
OH
OH
OH
More easily excreted than ROH itself
R
OH
Drug

52. Metabolism of Drugs (cont.)
• Another Phase II reaction is sulfation
(shown below)
NH2
N
O
O
R
OH
S
O-
N
O
O
P
O
N
O
O-
N
SO3R
Drug
O
O
P
OH
O-
O-
3'-Phosphoadenosine-5'-phosphosulfate
O
Sulfated Drug
(more easily excreted)

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

54. 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

55. •
•
•
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.

56. 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

57. 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

59. Birth defects
caused by use of thalidomide

60. 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.
O
N
O
NH
O
O
Thalidomide
presents at birth very short or absent long bones
and flipper-like appearance of hands and sometimes feet.
Phocomelia

61. Example: Thalidomide
•Researchers, however, continued to work with the drug. Soon
after its banishment, an Israeli doctor discovered antiinflammatory 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

62. 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.

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

64. 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.

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

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

67. Assigned Reading
• Haffner Marlene E; Whitley Janet; Moses Marie Two decades
of orphan product development. Nature reviews. Drug
discovery (2002), 1(10), 821-5. Link
• Franks Michael E; Macpherson Gordon R; Figg William D
Thalidomide. Lancet (2004), 363(9423), 1802-11. Link
• Abou-Gharbia, Magid. Discovery of innovative small molecule
therapeutics. Journal of Medicinal Chemistry (2009), 52(1),
2-9. Link
• Paul, S. M. et al. How to improve R&D productivity: the
pharmaceutical industry’s grand challenge. Nature Reviews
Drug Discovery (2010), 9: 203-214.
• Jorgensen, W. L. The many roles of computation in drug
discovery. Science (2004) 303: 1813-1818.
• Butcher, E. C. et al. Systems biology in drug discovery.
Nature biotechnology (2004) 22(10): 1253-1259.

68. Optional Additional Reading
• Bartlett J Blake; Dredge Keith; Dalgleish Angus G The
evolution of thalidomide and its IMiD derivatives as anticancer
agents. Nature reviews. Cancer (2004), 4(4), 314-22. Link
• Cragg, G. M.; Newman, D. J. Nature: a vital source of leads
for anticancer drug development. Phytochemistry Reviews
(2009), 8(2), 313-331. Link
• Betz, U. A. K. et al. Genomics: success or failure to deliver
drug targets? Current Opinion in Chemical Biology (2005), 9:
387-391
• Sams-Dodd, F. Target-based drug discovery: is something
wrong? Drug Discovery Today (2005) 10: 139-147.

69. Homework Questions
• What is an ‘orphan drug’. Why has the Orphan Drug Act been
successful?
• Thalidomide is actually a mixture of two compounds. Draw
their structures and list the physiological effects of each.
• What does ADMET stand for?
• List several possible reasons for poor efficacy of drug
candidates in in vivo models.
• Explain how structure-based design was used to develop an
inhibitor with improved selectivity for TACE over MMP-1 and
MMP-9.
• How can the pharmaceutical industry increase the probability of
technical success (p(TS))? What are the major causes of
Phase II and III attrition?