Drug Discovery and Development PHG 311 · Drug Discovery and Development PHG 311. To Learn the processes involved in ... – Computer aided design – Serendipity and prepared mind

Prof. Dr. Amani S. Awaad

Professor of PharmacognosyPharmacognosy Department,

College of Pharmacy Salman Bin Abdulaziz

University,

Al-Kharj. KSA.

Email: [email protected]

Drug Discovery and

Development

PHG 311

To Learn the processes involved in

drug discovery and development?

To understand The Drug Discovery

Process ?

To know what is Choosing a Disease

to know proses of Choosing a drug

tounderstand Finding a lead

compound

Overview of:

Drug Discovery Process.

Target identification and

selection

For R&D

The Drug Discovery Process

• Drug discovery is an expensive and time-

consuming.

• Retrospective analyses of the pharmaceutical

industry during the 1990s estimate that each

new drug in the market takes an average 14

years to develop, costing in the region of

$800 million

• In addition one in nine compounds that

enters clinical trials makes it to the

market.

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• For a drug to work, it has to interact with

a disease target (e.g. receptor, enzyme or

nucleic acid) in our body and intervene in

its way ward functions.

• An analogy is the lock and key

comparison, with the lock being the

disease target and the key representing

the drug. The correct key has to be found

to turn the lock and open the door to treat

the disease.

The Drug Discovery Process

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Drug discovery: Finding a leadWhen a pharmaceutical company or university research group initiates a new medicinal

chemistry project through to the identification of a lead compound, they will consider the

following steps in order

1-Choosing a Disease

-Disease Mechanism

III-Identifying a bioassayChoice of bioassay - In vitro test -In vivo testsTest validity -High-through screeningScreening by NMR -Affinity screeningSurface Plasmon resonance -Scintillation proximity assay

II-Choosing a drug target

Drug targets

Discovering drug targets

Target specificity and selectivity between species

Target specificity and selectivity within the body

Targeting drugs to specific organs and tissues

Pitfalls

Drug discovery: Finding a leadIV-Finding a lead compound

– Screening of natural products

– Medical folklore

– Screening synthetic compound “

libraries”

– Existing drugs

– Starting from natural ligand or

modulator

– Combinatorial synthesis

– Computer aided design

– Serendipity and prepared mind

– Computerized searching of structural

databases

– Designing lead compounds by NMR

VI-Structural determinationV-Isolation and purification VII-Herbal medicine

Most research is carried out on diseases whichafflict “first world” countries: (e.g. cancer,cardiovascular diseases, depression, diabetes, flu,migraine, obesity).

1-Choosing a Disease

The Drug Discovery Process cont..

• Pharmaceutical companies tend to concentrate

on developing drugs for diseases which are

prevalent in developed countries, and aim to

produce compounds with better properties than

existing drugs.

• Pharmaceutical companies have to consider

economic factors as well as medical ones when

they decide which disease to target when

designing a new drug.

• A huge investment has to be made towards the

research and development of a new drug.

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Disease Mechanism

1-Defines the possible cause or causes

of a particular disorder

2-Defines the path or phenotype of the

disease.

3-Understanding the disease mechanism

directs research and formulates a

possible treatment to slow or reverse the

disease process.

4-It also predicts a change of the disease

pattern and its implications.

Why The disease mechanism?


I- Choosing the disease

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Disease Mechanism Classifications of Disease mechanisms

5-Trauma and acute disease based

on injury or organ failure

1-Defects in distinct genes

—genetic disorders 3-Infection by bacteria,

fungi, or viruses 2-Immune/autoimmune disease

4-Multiple causal disease


I- Choosing the disease

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Target-identification, selection and mechanism-of-action studies have important roles in

small-molecule probe and drug discovery

Target identification and selection is the earliest phase of R&D in the drug discovery and

development (DD&D) value chain.

Making the right choice of targets at the beginning of the DD&D process is the crucial first step

down the long and expensive road of creating innovative medicines.


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The "drugability" of a given target is defined

either by

how well a therapeutic, such as small molecule

drugs or antibodies, can access the target,

or by

the efficacy a therapeutic can actually achieve.

A long list a parameters

influences drugability of

a given target;

these include: cellular

location, development of

resistance, transport

mechanisms such as

export pumps, side

effects, toxicity, and

others



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The term biological target is frequently used in pharmaceutical research to describe

the native protein in the body whose activity is modified by a drug resulting in a

specific effect, which may be a desirable therapeutic effect or an unwanted adverse

effect. In this context, the biological target is often referred to as a drug target.

The most common drug targets of currently marketed drugs include

•proteins

• G protein-coupled receptors

(target of 50% of drugs)[

• enzymes (especially protein

kinases, proteases, and

phosphatases)

• ion channels

• nuclear hormone receptors

• structural proteins

• membrane transport proteins

•nucleic acids


1.Drug target


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a. Target Identification

The starting point for a target-oriented drug-

discovery project is to identify a relevant target.

• The first requirement in

conventional drug discovery is

identification of a valid target, a

molecule which has a link with the

disease of interest, such that

pharmacological intervention

would be expected to cure the

disease or ameliorate its symptoms.



1.Drug target

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b. Techniques of Target Identification

There are a number of techniques used for target identification.

i)Radio ligand binding was a

common technique until recently.

ii) Now DNA microarrays,

expressed sequence tags are used

The Drug Discovery Process cont..II-Choosing a drug target

1.Drug target

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i)Radio ligand binding (RLBA)

1)The classic method to discover drug targets or

receptors is to bind the potential receptors with radio

ligands, so that targets can be picked out from a pool

of other receptors.

2)Bound receptors are then separated from the

radio ligands and sequenced.

3)Potential drug molecules are then studied with

these receptors or their nucleotide sequences to

determine their interactions in terms of

biochemical and functional properties.

II-Choosing a drug targetThe Drug Discovery Process cont..

1.Drug target

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ii) DNA microarrays.

• DNA microarray, also known as DNA or gene

chips, is a technology to investigate how

genes interact with one another and how they

control biological mechanisms in the body.

• The gene expression profile is dynamic and

responds to external stimuli rapidly. By

measuring the expression profile, scientists

can assess the clues for the regulatory

mechanisms, biochemical pathways, and

cellular functions.

• In this way, microarrays enable scientists to

find out the target genes that cause disease.

II-Choosing a drug targetThe Drug Discovery Process cont..

1.Drug target

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ii) DNA microarrays cont..

What is Microarrays?

• To use the microarray, a known

sequence of short DNA is printed on

a solid support of membrane or

glass slide.

• From healthy and diseased cells,

mRNAs are isolated.

• The mRNAs are used to generate

complementary DNAs (cDNAs).

• Fluorescent tags are attached to the

cDNAs, and the cDNAs are then

mixed and incubated with the

microarray supports (slides



1.Drug target

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c. Drug Target Selection

Once a therapeutic area has been identified,

the next stage is to identify a suitable drug

target (e.g. receptor, enzyme or nucleic acid)

Understanding which bio macromolecules

are involved in a particular disease state is

very important.

This will allow the medicinal chemist

whether agonist or antagonist to be

designed for a particular receptor or

whether inhibitors should be designed

for a particular enzyme.



1.Drug target

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b. Drug Target Selection cont..

Tricyclic antidepressants such as Desipramine

are known to inhibit the uptake of NA from

nerve synapses. However, these drugs also

inhibit uptake of serotonin, so the possibility

arose that inhibiting serotonin uptake might be

beneficial.

A search for selective serotonin uptake

inhibitors has led to the discovery of

Fluoxetine, the best selling antidepressant.

For example



1.Drug target

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2- Discovering drug targets

If a drug or a poison produces a biological effect, there must

be a molecular target for that agent in the body.

In the past, the discovery of drug targets depends on finding the

drug first. Then, natural chemical messengers started to be

discovered.

But many targets still stay hidden (orphan receptors i.e, novel

receptors whose endogenous ligand is unknown ) and their

chemical messengers are also unknown.

The challenge is to find a chemical that will interact with these

targets in order to find their function and whether they will be

suitable as drug targets.



This is one of the main driving forces behind the rapidly

expanding area of Combinatorial synthesis (synthesis of a large

number of compounds in a short period of time using different

reagents and starting material and are tested for activity.)

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3- Target specificity and selectivity between species



Target specificity and selectivity is a crucial factor in modern medicinal chemistry research.

The more the selective a drug is for its target, the less chance that it will interact with different

targets and have less undesirable side effects.

For example, penicillin target an enzyme

involved in bacterial cell wall biosynthesis.

Mammalian cells does not have a cell wall, so

this enzyme is absent in human cells and

penicillin has few side effects.

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4-Target specificity and selectivity within the body

• Selectivity is also important for drug acting on

targets within the body

• Enzyme inhibitors should only inhibit the target

enzyme and not some other enzyme.

• Receptors agonist/ antagonist should ideally interact

with a specific kind of receptor (adrenergic

receptor) rather than a variety of different receptors,

or even a particular receptor type ( such as β-

receptor) or even a particular receptor subtype β2-

receptor.

• Ideally, enzyme inhibitors should show selectivity

between the various isozymes of an enzyme.



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5-Targeting drugs to specific organs and tissues

• Targeting drugs against specific receptor subtypes often allows drugs to be targeted

against specific organ or against specific areas of brain.

• This is because the various receptor subtypes are not uniformly distributed around the

body, but are often concentrated in particular tissues.



For example, adrenergic

receptors in the heart are

predominantly β1 while

those in the lungs are β2. If

a drug acts on either, less

side effects would be

observed.

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6-Pitfalls

The body is a highly complex

system. It is possible to identify

whether a particular enzyme or

receptor plays a role in a particular

aliments.

For any given function, there are

usually several messengers, receptors,

and enzymes involved in the process

Sometimes, more than one target may

need to be addressed for a particular

ailment



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6-Pitfalls

There is no one simple cause for

hypertension, there are variety of

receptors and enzymes which can be

targeted in its treatment. These

include β1-adrenoceptors, calcium

ion channels, angiotessin-converting

enzyme (ACE), and potassium ion

channels.

Example



For example, most of the current

therapies for asthma involve a

combination of bronchodilator (β2

agonist) and an anti-inflammatory

agent such as a corticosteroid

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1-Choice of bioassay

III-Identifying a bioassay

Choosing the right bioassay or test system is crucial to the success of a drug research .So it needs

the following

The test should be simple, quick and relevant

Human testing is not possible at such

early stage

in vitro first. Because in vitro testsare cheaper, easier to carry out,less controversial and can beautomated than in vivo one.

In vivo tests needed to check the drugs

interaction with specific target and to monitor

their pharmacokinetics properties



2-In vitro tests

They do not involve live animals. Instead, specific tissues, cells, or enzymes are isolated and used.

Enzyme inhibitors

can be tested on pure

enzyme in solution

Receptor agonist

and antagonists

can be tested on

isolated tissues or

cells.

Antibacterial drugs

are tested in vitro by measuring

how effectively they inhibit or kill

bacterial cells in culture

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• In vivo tests on animals often involve inducing a clinical

condition in the animal to produce observable symptoms.

• The animal is then treated to see whether the drug

alleviates the problem by eliminating the observable

symptoms. For example, the development of non-steroidal

inflammatory drugs was carried out by inducing

inflammation on test animals.

• The animals used may be transgenic. i.e,some mouse

genes are replaced by human genes so the mouse produces

the human receptor or enzyme. Or the mouse’s gene may

be altered to be susceptible for some disease such as breast

cancer.



3-In vivo tests

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There are several problems associated with in vivo

testing.

• It is slow

• causes animal suffering.

• many problems of pharmacokinetics and the result

obtained may be misleading.

For example, penicillin methyl ester is hydrolyzed in

mice into active penicillin, while it is not hydrolyzed in

humans or rabbits. Also, thalidomide is teratogenic in

rabbits and humans while it is not in mice.



3-In vivo test

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• Sometimes the validity of testing procedure is easy and

clear.

For example,

the antibacterial drug can be tested by its effect on killing

bacteria.

Local anesthetics are tested by their effect on blocking

action potential in isolated nerve.

• In other cases, the testing procedure is more difficult.

For example,

there is no animal model for antipsychotic drug.

Thus, validity of the test should be carried out.



4-Test validity

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5-High throughput screening (HTS)

HTS involves the miniaturization and

automation of in vitro tests such that

a large number of tests can be carried

out in a short period of time.

It involves testing of large number of

compounds versus a large number of

targets.

The test should produce easily

measurable effect. This effect may be

cell growth, an enzyme catalyzed

reaction which produces a color

change (may be a dye) or displacement

of radioactive labelled ligand from its

receptors.

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• NMR was used as a tool for determining the

molecular structures of compounds

• Recently, compounds can be tested or screened

for their affinity to a macromolecular target by

NMR spectroscopy. The relaxation times of

ligands bound to a macromolecule are shorter

than when they are unbound (can’t be detected).

• In NMR spectroscopy the compound is radiated

with a short pulse of energy which excites the

nuclei of specific atoms (H,N,C) afterwards, the

excited nuclei slowly relax back to the ground

state giving off energy as they so.



6-Screening by NMR

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• There are, several advantages in using NMR

as a detection system:

1-It is possible to screen 1000 small molecular

weight compounds a day with one machine.

2-The method can detect weak binding which would

be missed by conventional screening methods.

3-It can identify the binding of small molecules to

different regions of binding site.

4-It is complementary to HTS. The later may give

false-positive results, but these can be checked by

NMR to ensure that the compounds concerned are

binding in the correct binding site.



6-Screening by NMR

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5-The identification of weakly binding molecules

allows the possibility of using them as building

blocks for the construction of larger molecules

that bind more strongly.

6-Screening can be done on a new protein

without needing to know its function.

• NMR screening also has limitations, the main

one being that at least 200 mg of the protein

required.



6-Screening by NMR

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SPR (change in

refractive index)&

SPR (reduction of

emission of light) are

two visual methods of

detecting whether

ligands bind to

macromolecular

targets .



7-Surface Plasmon resonance (SPR) & scintillation proximity

assay (SPA)

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Drug Discovery and Development PHG 311 · Drug Discovery and Development PHG 311. To Learn the processes involved in ... – Computer aided design – Serendipity and prepared mind