Drug Discovery and

Development

How are drugs discovered and developed?

• 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)

• Synthesize analogs of the lead

• Identify Structure-Activity-Relationships (SAR’s)

• 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.

• Patent the drug

• Continue to study drug metabolism

• Continue to test for toxicity

• Design a manufacturing process

• Carry out clinical trials

• Market the drug

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)

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)

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).

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

• Sometimes this can happen through

incidental observation…

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).

N H 2

NH

H O

s e ro to n in

O

H N

p ro z a c

N

NC H 3

H 3C

Im ip ra m in e

(a c la s s ic a l t r ic y c lic a n tid e p re s sa n t)

F 3 C

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.

• 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.

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.

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

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.

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.

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.

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

Choosing the Bioassay (cont.)

In vivo tests

• More expensive

• May cause suffering to animals

• Results may be clouded by interference

with other biological systems

Finding the Lead

Screening Natural Products

• Plants, microbes, the marine world, and

animals, all provide a rich source of

structurally complex natural products.

• 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

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

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).

Finding the Lead (cont.)

Enhance a side effect

O

N H

S

O

O

N H

to lb u ta m id e

N H 2S

O

O

H 2 N

s u lp h a n ila m id e

(a n a n t ib a c te r ia l w ith th e s id e e f fe c t o f

lo w e r in g g lu c o s e le v e ls in th e b lo o d a n d a ls o

d iu re tic a c tiv i ty )

(a c o m p o u n d w h ic h h a s b e e n o p tim iz e d to o n ly

lo w e r b lo o d g lu c o se le v e ls . U s e fu l in th e t re a tm e n t

o f T y p e I I d ia b e te s .)

S

N H

N

O O

S

O

OH 2 N

C l

C h lo r o th ia z id e

(a c o m p o u n d w h ic h h a s b e e n o p tim iz e d to o n ly d is p la y d iu re tic

a c t iv ity .)

Use structural similarity to a natural ligand

N

N H 2

H O

H

N

N (C H 3 )2

H

S

HN

O O

H 3 C

5 -H y d r o x y tr y p ta m in e (5 -H T )

S e ro to n in (a n a tu ra l n e u ro tra n sm it te r

sy n th e s iz e d in c e r ta in n e u ro n s in th e C N S )

S u m a tr ip ta n (I m itr e x )

U se d to tre a t m ig ra in h e a d a c h e s

k n o w n to b e a 5 -H T 1 a g o n is t

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.

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

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.

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.

Finding a Lead (cont.)

N

N

S

O

O

N

N

N

N H

O

O

v ia g ra

(S ild e n a f i l)

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

• 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

Link

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,%20Meta

bolism%20and%20Excretion%20Animation&

publication_ID=2450

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 (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

Mechanism of Cytochrome

P450

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

The Liver

• Oral administration frequently brings the

drugs (via the portal system) to the liver

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

O HH O

O H

H O

O PH O

O

O

P

H OO

O O

H O

O H

N

N H

O

O

R O H

O O

O HH O

O H

H O

O

R

G lu c u ro n ic A c id

U D P G lu c u ro n ic A c id

M o re e a s i ly e x c re te d th a n R O H i ts e l f

g lu c u ro n o s y l tra n s fe ra se

e n z y m e

D ru g

D ru g

Metabolism of Drugs (cont.)

• Another Phase II reaction is sulfation

(shown below)

R O H

O N

N

N

N

N H 2

O HO

OP

O

O-

OS

O

O

O-

PO O-

O-

3 '-P h o s p h o a d e n o s in e -5 '-p h o sp h o su lfa te

D ru gR O

S O 3-

S u lfa te d D ru g

(m o re e a s ily e x c re te d )

Phase II Metabolism

• Phase II reactions most commonly

detoxify

• Phase II reactions usually occur at polar

sites, like COOH, OH, etc.

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

• 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.

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

Example: ThalidomideThalidomide 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

Birth defects

caused by use of thalidomide

Example: ThalidomideFrom 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

N H

O

O

T h a lid o m id e

Phocomelia presents at birth very short or absent long bones

and flipper-like appearance of hands and sometimes feet.

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

ThalidomideFurther 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.

Clinical Trials• Phase I: Drug is tested on healthy volunteers

to determine toxicity relative to dose and to

screen for unexpected side effects

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.

Clinical Trials

• Phase III: Drug is tested on much larger

group of patients and compared with existing

treatments and with a placebo

Clinical Trials

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