drug discovery and development

5/21/2018 Drug Discovery and Development

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University of Tripoli

Faculty of pharmacy

developmentdevelopment3 rd ear harmac

S. M. Bensaber

Tripoli

2013 / 2014 1

DEVELOPMENT OF DRUGS ( DRUG DESIGN ) 12hrs

A- Sources of Drugs.

1- Natural sources

2- Semisynthetic drugs

3- Synthetic drugs.

B- Genesis of Drugs.

1- Serendipity ( Accidental discovery )

- .

i- Rationally directed random screening .

ii- Rationally directed metabolite approach .

3- Extraction from natural sources.

4- Molecular modifications

i- General processes. ii- Special processes.

- Simplification ( Disjunction).-Replication.

- Hybridization.

-Addition.

-Vinylogy principle- Increase or decrease of the alkyl chain .

- Isosteric substitution ( isosteres and bioisosters).

- Introduction of a bulky group .

C- Soft and hard drugs .

D- Drug latentiation .

- Prodrugs - Bioprecursors - Targeted drugs

E- Anti metabolite approach .

- .

- Others .

iii- Methods of lead optimization.- Topless sequential method ( pi , sigma , Es)

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Drug Discovery & Development:

Human clinical trials

(2-10 years)The discovery phase

The Clinical phase

3

FDA approval

(2-3 years)

Identify disease

The discovery phase

Drug Discovery & Development:

The drug discovery is a lengthy,

expensive, and complicated process,

and validation

Lead discovery &optimisation

Processing

chemistry

that requires the collaboration of a

large number of research scientists

with skills ranging from computational

and structural chemistry, through

synthetic organic chemistry, molecular

Pre-clinical testing

In vitro


In vivo

cell biology, genomics, proteomics,

physiology, pharmacology, toxicology,

and clinical biochemistry, amongst

others.4


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Identify disease

Selection of a disease target:

Acceptable therapies are available today for many conditions,

e.g. (Antibiotics for bacterial diseases etc, paracetamol /

ibuprofen etc. for moderate pain relief).

New agents must have statistically proven clear advantages

over existing therapy (not just that it is clinically effective).

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Target identification

and validation

A bio(macro)molecule may be involved in a disease

process, but to be a drug target it has to be validated.

In other words shown to be critical in the disease process.

Useful techniques available are to validate a target such as

Gene knockout and RNA interference.

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Alead compound isa compound from a series of related

Lead discovery &

optimisation

.

This molecule can be characterised, and modified to

produce another molecule with a better profile of wanted

properties to unwanted side effects.

Alead compound is a first foothold on the drug discovery

ladder.

It takes much more effort to make alead compound into a

drug candidate7

TESTING DRUGS

Biological tests are required in order to find lead

compounds and for drug optimisation

Tests can bein vivo orin vitro

A combination of tests is often used in research

programmes


In vitro


In vivo

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Tests not carried out on animals/humans

Tests carried out on target molecules (enzymes or receptors)

Cells e. . cloned cells


In vitro

Tissues (e.g. muscle tissue)

Organs

Micro-organisms (for antibacterial agents)

More suitable for routine testing

Measure the interaction of a drug with the target but not the

ability of the drug to reach the target

Does not demonstrate a physiological or clinical effect(s)

Does not identify possible side effects and effective prodrugs 9

Identify competitive or non competitive inhibition

Enzyme Inhibition Tests


In vitro Examples

Strength of inhibition measured as IC50

IC50= concentration of inhibitor required to reduce enzyme

activity by 50%

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Not easy to isolate membrane bound receptorsNot easy to isolate membrane bound receptors

Testing with Receptors


In vitro Examples

Carried out on whole cells, tissue cultures, or isolated organsCarried out on whole cells, tissue cultures, or isolated organs

AffinityAffinity -- strength with which compounds bind to a receptorstrength with which compounds bind to a receptor

EfficacyEfficacy -- measure of maximum biochemical effect resultingmeasure of maximum biochemical effect resulting

from binding of a compound to a receptor.from binding of a compound to a receptor.

PotencyPotency -- concentration of an agonist required to produceconcentration of an agonist required to produce 5050%%of the maximum possible effect.of the maximum possible effect.

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In vivo

Carried out on live animals or humans

Measure an observed h siolo ical effect

Measure a drugs ability to interact with its target and its

ability to reach that target

Can identify possible side effects

Transgenic animals - genetically modified animals

Drug potency

Therapeutic ratio/index -

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1- Natural sources, 2- Semisynthetic drugs, 3- Synthetic drugs.

Sources of Drugs.

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TARGET DISEASE

Priority for the Pharmaceutical Industry

Can the profits from marketing a new drug outweigh the

cost of developing and testing that drug?

Questions to be addressed

Is the disease widespread?(e.g. cardiovascular disease, ulcers, malaria)Does the disease affect the first world?

(e.g. cardiovascular disease, ulcers)

Are there drugs already on the market?

If so, what are their advantages and disadvantages (e.g.

side effects)

Can one identify a market advantage for a new therapy?

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DRUG TARGETS

A) Lip idsCell membrane lipids

B Proteins

Receptors

Enzymes

Carrier proteins

Structural proteins (tubulin)

C) Nucleic acids

DNA

RNA

D) Carbohydrates

Cell surface carbohydrates

Antigens and recognit ion molecules

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DRUG TARGETS

Between species

Target selectiv ity

,

Identify targets which are unique to the invading

pathogen

Identify targets which are shared but which are

significantly different in structure

Within the bod

Selectiv ity between different enzymes, receptors etc.

Selectivity between receptor types and subtypes

Selectiv ity between isozymes

Organ and t issue selectivity

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The Lead Compound

A compound demonstrating a property likely to betherapeutically useful

The level of activity and target selectivity are not crucial

Used as the starting point for drug design and development

Found by design (molecular modelling) or by screening

compounds (natural or synthetic)

ee o en y a su a e es n or er o n a ea compoun

Active Principle - a compound that is isolated from a natural

extract and which is principally responsible for the extracts

pharmacological activity. Often used as a lead compound.17

Sources of Lead Compounds

A) The Natural World Plantlife (flowers, trees, bushes)Micro-organisms (bacteria, fungi)

Animal li fe (frogs, snakes, scorpions)

Biochemicals (Neurotransmitters, hormones)

B) The Synthet ic World

Marine chemistry (bacteria, fish etc)

Chemical synthesis (traditional)

Combinatorial synthesis

C) The Virtual World

Computer aided drug design

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Identif ication of Lead Compounds

A) Isolation and purificationSolvent-solvent extraction

Chromatography

Distillation

B) Structure determination

Elemental analysis

Molecular weight

Mass s ectrometr

Infra red spectroscopyUltra violet spectroscopy

MNR (1H,13C,2D) spectroscopy

X-Ray crystallography

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1- Natural product screening

I- Discovery and structural modification

of lead compounds

A- Discovery of lead compounds

2- Drug discovery via random screening of synthetic

organic compounds3- Drug discovery via targeted dedicated screening and

rational design

-

5- Drug discovery from the observation of side effects

6- Pharmacophore-based drug design

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PLANT EXTRACTS

-


CINCHONA BARK - Quinine

YEW TREE - Taxol

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PLANT EXTRACTS

WILLOW TREE - SALICYLIC ACID


COCA BUSH - COCAINE

AspirinOH

O OHAceticanhydride O

O OH

CH3

O

Procaine

N

O

H

H

CO2Me

C

O

O

C

O

N

NH2

CH3

CH3

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MICRO-ORGANISMS

S CH3

HHHN

R

O

OOHOOH O

NH2

OHH2N C

HN

NHHN C

NH

NH2H

OHH HO

HH

H


CH3O

CO2H

S

HN H HC

O

R

Cl

OH

NMe2HO Me H

O2N

CH2OH

HO H

OO

OO

H

CHO

OH

H

Me

CH2OH

H

HO

H

OH

H

H

MeHN

H

HPENICILLIN TETRACYCLINES

N OAc

CO2HO

HN H

CO CHCl2

CEPHALOSPORINS

STREPTOMYCIN

CHLORAMPHENICOL

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VENOMS AND TOXINS

C

O

NH

CH C

OHN CH C

O

N

C

O

N

C OH

O

TeprotideTeprotide


H2N CH C

CH2

O

CH2

C

OH

O

NH

CH C

CH2

O

HN

N

C NH

CH C

CH2

CH2

CH2

NH

C

NH2

NH

N

CH2

CH2

C

NH2

O

CHCH3

CH2

CH3

O

C OH

O

Captopril

(anti-hypertensive)

CH3

C N

HS

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ENDOGENOUS COMPOUNDS NATURAL LIGANDS FOR RECEPTORSNATURAL LIGANDS FOR RECEPTORS

HOHN

Me

OH

HO

OHHN

A onistA onist


HO

ADRENAL INE

HO

SALBUTAMOL

O NH

OH

AntagonistAntagonistHO

HO

HN

Me

OH

PROPRANOLOLADRENALINE

HNN

Me

S

HN NHMe

CN

CIMETIDINE

HNN

NH2

HISTAMINEAntagonistAntagonist

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2- Drug discovery via random screening of synthet ic

organic compounds

Random screening- only approach before 1935; screen

every compound you have; still a useful approach;

streptomycin and tetracyclines identified in this way

High-throughput Screens (HTS)

Very rapid, sensitive in vitro screens

Can assay 100,000 compounds a day

1990 ~ 200,000 compounds screened per year

~ - compoun s screene per year

2000 > 50 106 compounds screened per year

in a large pharmaceutical company

So far, no increase in rate of the number of drugscoming on the market.

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3- Drug discovery via targeted dedicated screening and

rational design

Nonrandom (or Targeted or Focused) screening - only

screen compounds related to active compounds

Rational approaches- identify causes for disease states:

imbalance of chemicals in the body

invasion of foreign organisms

aberrant cell growth

Structure-Activity Relationships (SARs) & Molecular modelling

use natural receptor ligand or enzyme substrate as the lead;

a known drug also can be used as a lead

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4- Drug discovery via metabolism studies

Drug metabolism studies - metabolites produced are

screened for the same or other activities

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Clinical observations- new activities found in clinical trials;

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Determine the effects of structural changes on activity ofdrug:structure-activity relationships (SARs)


the molecule containing the essential organic functional

groups that directly interact with the target active site and

therefore, confers on the molecule the biological activity of

interest.

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If ou know the harmaco hore for our tar et, ou can

Design new structures.


Design: use analyzed data to design new compounds -

hopefully with better properties

Why make new lead compounds? Increase activity (make binding stronger)

Decrease side effects (increase selectivity)

Improve ease and efficiency of administration to patient

Potentiall find a better s nthetic route

create new lead compounds based on the pharmacophore!

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Simple example 1: 3D structures are known (active molecule)1. Data collection: biological activity of lead compound (and

other compounds)


.

pharmacophoric features (superimpose 3D structures & findcommon features)

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Simple example 1:

3. Design new structures. New molecular mimic will be

tested.

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- Simplification ( Disjunction).

i- General processes.

I- Discovery and structural modification of lead

compounds

B- Molecular modifications of lead compounds

-Replication.

- Hybridization.

-Addition.

-Vinylogy principle

- Increase or decrease of the alkyl chain .

ii- Special processes.

- .

- Electron withdrawing and electron donating groups.- Others .

iii- Methods of lead optimization.- Topless sequential method ( pi , sigma , Es)

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1- Simplification ( Disjunction).


Once a biologically active compound is found, a common first method is


Example: ergot alkaloids like

to simplify it to determine the essential parts for activity.

For complex molecules, this often leads to easier synthesis.

Will not be successful if all parts of the molecule are needed for activity

bromocriptine were starting points

for simplified synthetic analogs

shown below

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Synthesis & Evaluation simpler analogs of lead compound Ex. Opioid

1- Simplification ( Disjunction).i- General processes.


through simplification of cocaine

Morphine Cocaine

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1- Simplification ( Disjunction).


Molecular modif ications

Morphine

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2- Molecular Replication & Hybridizationi- General processes.

-The association of two identical pharmacophoric entities will


generate an "identical twin drug" which is equivalent to a

homodimer derivative.

-A compound, where two different pharmacological entities are

bounded, is called a "non-identical twin drug" or heterodimer.

- e rs es gn s ra egy s equ va en o a up ca on

dimerization process of an active compound or lead.

-The aim of this approach is the production of a more potent

and/or more selective drug compared to the single entity.

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2- Molecular Replication & Hybridization


dual acting drugs

symbiotic approach

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4- Molecular addition:i- General processes.

Weak forces as (electrostatic and hydrogen bonding)

+


.

Methenamine

N

O+

Methenamine Mandelate

Mandelic acid

N NH

N

OH

O

-

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1- Increase or decrease of

the alkyl chain .

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2- Vinylogy principle


-The vin lo rinci le was first formulated b Claisen in 1926 who


observed for formylacetone acidic properties similar to that of acetic acid.

-The vinyl group plays the role of an electron-conducting channel

between the carbonyl and the hydroxyl group.

-The same effect explains the acidity of ascorbic acid.

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2- Vinylogy principle



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3- Isosteric substitution ( isosteres and bioisosters).ii- Special processes.

Common alterations of compounds: replacement of groups with


Examples:

OH isosteres: SH, NH2, CH3O isosteres: S, NH, CH2H isostere: F

O NH

NH

.

Isosteres: atoms or groups of atoms which have the same valence

amide pyrrole

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Classical and non-classical bioisosteres

for the classical ones, where size equivalence is the key, the



.

The key replacements (for example, the C, O, and N replacements are

seen for three of the classical isosteres: CH3-,- OH,- NH2 for univalent;

-CH2-, -O-, and -NH- for divalent;

and -COCH2-R (ketone), -COOR (ester), and- CONHR (amide) for the

carbonyl containing compounds.

You should also be able to make isosteric replacements for the ring

equ va en s s ng e aroma c r ngs; s ng e a p a c r ngs, or e genera

tricyclic replacement).

For example we could change the ester alcohol oxygen (not the carbonyl

oxygen) with a CH2 (ketone), NH (amide), or S (thioester).

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If you change an O to CH2- sterics same, but no dipole or lone pair

3- Isosteric substitution ( isosteres and bioisosters).ii- Special processes.


you c ange an o - s er cs eren , u s a one pa r

O NH

NH

OH

S NH

OH

no activity

Example

Propranolol (beta blocker)NH

OH

HN NH

OH

no activity

no activity active(but less thanPropranolol)

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3- Isosteric substitution ( isosteres and bioisosters).


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Common alterations of compounds: replacement of groups with

ii- Special processes.3- Isosteric substitution ( isosteres and bioisosters).


bioisosteres.

Bioisosteres - different chemical groups with the same biological activity.

No restriction on sterics and electronics, unlike classical isosteres.

O N

HOH

Propranolol (beta blocker)potent

HOH

Pindololvery potent

NH

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3- Isosteric substi tution ( isosteres and bioisosters).


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ii- Special processes.4- Ring expansion/contractions - changes geometry


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5- Ring variations - may add a binding interaction with

heteroatom;



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6- Extend structure by adding a funct ional group to lead

compound



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7- Extend or contract linking chain length between groups



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-Limit number of possible conformations

-


8- Rigidification


-Locks molecule in most active conformation - more effective

Add a ring

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8- Rigidification


r g groups

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Add a bulky groups affect conformation; it may affect steric


8- Rigidification


.

Alter Stereochemistry: usually

different stereoisomers have

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H-bond donor or acceptor

Convert to:

II - Binding role of specific functional groups in a molecule

Binding role of hydroxyl groups:

Methyl ether (no H-bond donor now; may cause steric problem)

An ester (no H-bond donor; poor H-bond acceptor; steric problem)

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Methyl ether (no H-bond donor; still H-bond acceptor; may cause steric

problem)

Binding role of hydroxyl groups:


An ester (no H-bond donor now; poor H-bond acceptor; may cause steric

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H-bond donor (if N-H is present) or acceptor; ionic (protonation of N to

Binding role of amino groups:


Convert to:

Amide (no protonation; no H-bond acceptor now; steric problem).

Tertiary amine (no H-bond donor now; still H-bond acceptor; steric).

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Hydrophobic;

Convert to:

Saturated compound (not effective overlap; no pi system; more flexible).

Binding role of aromatic rings, alkenes:


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H-bond acceptor; dipole-dipole

Convert to:

Alcohol eometr chan e can weaken H-bond or di ole-di ole

Binding role of ketones:


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Hydrophobics/sterics

Convert to:

Longer (homologation) or differently-branched groups

Binding role of alkyl substituents:


Alkyl groups most easily modified are

DRUG OR DRUG

O

OR

DRUG

O

R

O

DRUGO

R

HN DRUG

O

NR2

DRUG NCH3

R

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Notes:

Recall impact of lipophilicity on drug transport through body

Changing alkyl groups may also affect the preferred conformation of the

molecule!

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Example: Nifedipine analogs

CH3



O2N

N CH3H3C

CO2CH3H3CO2C

H

O2N

N CH3H3C

CO2CH3H3CO2C

H

O2N

N CH3H3C

CO2CH3H3CO2C

H

CH3

Chemical synthesis of analogs help validate or refute hypotheses

regarding mechanism of action/mode of binding - part of design

NifedipeneTreats hypertension

Inactivesteric "bump"

InactiveDifferent conformation

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various/ sterics

Convert to:

Same substituents at different locations

Binding role of aryl substituents:


Substituents may affect each others properties (pKa)

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Binding role of aryl substituents:


ONR

6

8

7

-Best when substituent was at position 7

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H-bond acceptor; dipole-dipole

Convert to:

Hydrolysis products (but will lose a piece); reduce (no more H-bond

Binding role of amides:


acceptor

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II - Prodrug The term prodrug, which was used initially by

Albert HI, is a pharmacologically inactive

compound that is converted into an active drug

by a metabolic biotransformation.

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Prodrug can be classified to two classes:

(1) Carrier linked prodrug- Temporary linkage of the active molecule with transport moiety

- Mostly of lipophilic nature

-

- Non toxic

- Ability to ensure the release of active principle

(2) Bioprecursors

- Do not imply a temporary linkage between the active principle & carrier

- Result from molecular modification of active principle- This modification generate new compounds able to be a substrate for the

metabolizing enzymes.

- Metabolite being the expected active principle

- Ability to ensure the release of active principle75

Prodrug

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Prodrugs for improved lipophilicity or permeability

Prodrug: Why

Prodrugs for improved parenteral administration

Prodrugs to exploit carrier-mediated absorption

Prodrugs for other purposes

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Prodrugs for improved lipophilicity or permeability

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Prodrugs for improved aqueous solubility

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Prodrugs for improved parenteral administration

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Prodrugs to exploit carrier-mediated absorption

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Prodrugs for improved ophthalmic and dermal delivery

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Prodrugs for other purposes

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Soft Drugs - These are the oppositeof prodrugs. Thesecompounds are designed and synthesized as ACTIVEACTIVEcompounds that readily undergo metabolic inactivation to

IV - Soft & Hard Drugs

nontoxic products

Hard Drugs - compounds that contain structuralcharacteristics required for activity but are not susceptibleto metabolism

Increased efficiency by avoiding metabolism

o tox c meta o tes are orme

HOWEVER, less readily eliminated due to lack ofmetabolism

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A- Soft Drug

Soft drugs are biologically active drugs

designed to have a predictable and controllable

metabolism to nontoxic and inactive products

after they have achieved their desired

pharmacological effect.

The molecule could be deactivated and

detoxified shortly after it has exerted its

biological effect, the therapeutic index could be

increased, providing a safer drug.85

Advantages of Soft Drug

Elimination of toxic metabolites, thereby increasing the

therapeutic index of the drug;

Avoidance of pharmacologically active metabolites that

can lead to long-term effects; Elimination of drug interactions resulting from

metabolite inhibition of enzymes;

Simplification of pharmacokinetic problems caused by

multiple active species.

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The difference between prodrugs

and soft durgs

The concepts of prodrugs and soft drugs are opposite, as

follow:

A prodrugs is an inactive compound that requires a

metabolic conversion to the active form;

A soft drug is pharmacologically active and uses metabolism

as a means of promoting excretion.

However, it is possible to design a pro-soft drug, a modified

soft drug that requires metabolic activation for conversion to

the active soft drug.

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B- Hard Drugs

Hard drugs are nonmetabolizable compounds,

characterized either by high lipid solubility and

accumu a on n a pose ssues an organe es or

high water solubility. They are poor substrates for the metabolizing

enzymes; the potentially metabolically sensitive

parts of these drugs are either sterically hindered or

the hydrogen atoms are substituted with halogens

to block oxidation.88


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V - QSAR

Quantitative structure-activity relationships

(QSAR) represent an attempt to correlate

structural or property descriptors of compounds

with activities.

These physicochemical descriptors, which include

arameters to account for h dro hobicit

electronic properties, and steric effects, are

determined empirically or, more recently, by

computational methods.89

Activities used in QSAR include chemical

measurements and biological assays.

disciplines, with many pertaining to drug design

and environmental risk assessment.

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VI - Molecular Modeling

A technique for the investigation of molecular structures and

properties using computational chemistry and graphical

visualization techniques in order to provide a plausible

three-dimensional representation under a given set of

circumstances.

Computer simulation of molecular structure, to predict and

sp ay s ape, ca cu a e m n mum energy con orma ons

and dynamic ranges, predict recognition sites, binding

orientations, etc.

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In Silico Design and Virtual Screening Techniques

Several computational chemistry approaches are based on the

availabilities of the target protein structures and known active ligands.

DOCK Receptor-Based Approach

When receptor and ligand structures are both known, the docking

receptor-based approach is the most ideal situation.

The ligand can be docked into the known receptor site and molecularmechanics used to simulate receptorligand interactions and dynamics.

Combinatorial-Based Approach

en recep or an gan s ruc ures are o un nown, v r ua

combinatorial chemistry approaches are used.

In this case, computational chemistry is used both to generate

structures and in parallel to perform chemical similarity and diversity

search analysis before and after combinatorial chemistry-based

experimental HTS.92


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Ligand-Based Approach

When the receptorstructure is unknownbut the ligandstructures are

known, a ligand-based approach is used. This situation represents the

most common case.

De Novo Design-Based Approach

When receptor structure is known and ligand structures are

unknown, de novo design-techniques are used.

In this situation, there is available information about the tar et

receptor, or a similar receptor, but no existing leads that can interactwith the active receptor sites.

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drug discovery and development

Documents

es25212018 drug discovery

drug target

drug optimisationtests

drug discoveryladder

d drug latentiation

clinical biochemistry

disease target

human clinical trials2