Rationale : Endogenous lead compounds often simple and flexible (e.g. adrenaline)Endogenous lead...

Rationale : • Endogenous lead compounds often simple and flexible (e.g.

adrenaline)• Fit several targets due to different active conformations

(e.g. adrenergic receptor types and subtypes)

10 .Rigidification

• Rigidify molecule to limit conformations - conformational restraint

• Increases activity (more chance of desired active conformation)• Increases selectivity (less chance of undesired active

conformations)

Disadvantage:• Molecule more complex and may be more difficult

to synthesise

Flexiblechain

single bondrotation

+ +

Different conformations

Methods - Introduce ringsBonds within ring systems are locked and cannot rotate freely

10 .Rigidification

Test rigid structures to see which ones have retained active conformation

HNX

CH3

X NHMe X

NHMe

X

MeN

X

NMe

X

NHMe

Introducingrings

Examples - Combretastatin (anticancer agent)

10 .Rigidification

More active

Less active

Rotatablebond

H3CO

H3CO

OCH3

OCH3

OH

Combretastatin A-4

Z-isomerOH

H3CO

H3CO

OCH3

OCH3

OH

Combretastatin

H3CO

H3CO

OCH3

OCH3

OH

E-isomer

Methods - Steric Blockers

10 .Rigidification

YX

Flexible side chain

X

Y

Coplanarity allowed

X

Y

CH3

Orthogonal ringspreferred

YX

CH3

steric block

Introduce steric block

X

Y

CH3

H

steric clash

Introduce steric block

X

CH3

Y

Unfavourable conformation

Stericclash

Rationale (isosteres) :

• Replace a functional group with a group of same valency (isostere) e.g. OH replaced by SH, NH2, CH3

O replaced by S, NH, CH2

• Leads to more controlled changes in steric/electronic properties

• May affect binding and / or stability

11. Isosteres and Bio-isosteres

a-Classical Isosteres, they are divided into five classes as illustrated in the following table:

Class 1)monovalent(

2)divalent(

3)trivalent(

4)tetravalent(

5)rings(

F,Cl,Br,IOH,SH

NH2, PH2

CH3

-O--S--Se--Te-

-N=-P=-As=-Sb=-CH=

=C==Si==N+==P==As==Sb+=

-CH=CH-S--O--NH-

Grimm's Hydride Displacement Law

C N O F Ne Na

CH NH OH FH -

CH2 NH2 OH2 FH2+

CH3 NH3 OH3+

CH4 NH4+

It is an early hypothesis to describe bioisosterism, the ability of certain chemical groups to function as or mimic other chemical groups.According to Grimm, each vertical column (of Table below) would represent a group of isosteres.

Table 1: Grimm's Hydride Displacement Law

• 1) Classical Isosteres: - Replacement of univalent atoms and groups

Replacement of CH3 group of the oral hypoglycemic tolbutamide, by its monovalent isostere Cl in chloropropamide increases the duration of action.

Examples

Interchange of divalent atoms or groups

• The replacement of -O- of procaine by -NH- in procainamide leads to prolong antiarrhythmic action due to the considerable stability of the amide function over the ester function.

Introduction of trivalent atoms or groups

• Aminopyrine and its isostere are about equally active as antipyretics.

Ring equivalents

NH

O S

b- Nonclassical Isosteres, they are also known and include paired examples such as H and F, -CO2H and –SO3H, and –CO- and –SO2-. Some of the examples of isosteric replacement that have provided useful drugs are include:

NH

N H

O

O

H

NH

N H

O

O

F

U r a c i l 5 - F U

N

N NH

N

O H

N

N NH

N

SH

H y p o x a n t h i n e 6 - M P

H2N CO2H H2N SO2NH2

PABA Sulfanilamid

Isosterism and Bioisosterism is a lead modification approach that has been shown to be useful to :

• Attenuate Toxicity• Modify the activity of a lead• May have a significant role in the alteration of metabolism of

the lead

Useful for SAR

• Replacing OCH2 with CH=CH, SCH2, CH2CH2 eliminates activity

• Replacing OCH2 with NHCH2 retains activity• Implies O involved in binding (HBA)

11 .Isosteres and Bio-isosteres

Propranolol (b-blocker)

OH

OH

NH

Me

Me

Structure based drug design (SBDD)

Procedure• Crystallise target protein with bound ligand

(e.g. enzyme + inhibitor or ligand)• Acquire structure by X-ray crystallography• Identify binding site (region where ligand is bound)• Identify binding interactions between ligand and target

(modelling)• Identify vacant regions for extra binding interactions

(modelling)• ‘Fit’ analogues into binding site to test binding capability

(modelling)

StrategyCarry out drug design based on the interactions between the lead compound and the target binding site

Design of Antihypertensives - ACE inhibitors

• ACE = Angiotensin converting enzyme• Angiotensin II

- hormone which stimulates constriction of blood vessels - causes rise in blood pressure

• ACE inhibitors - useful antihypertensive agents• ACE - membrane bound zinc metalloproteinase not easily

crystallised• Study analogous enzyme which can be crystallised

Structure based drug design

Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu

Angiotensin I

Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

Angiotensin II

His-LeuACE

+

Carboxypeptidase


-aa3-aa2-aa1Carboxypeptidase

+Peptide -aa3-aa2PeptideCO2H CO2H aa1

L-Benzylsuccinic acid

OH

O

O

OH

Inhibition

Carboxypeptidase mechanism


Natural Substrate

R NH

O

O

O

Zn2+

S1' pocket

NH2

H2N

145

Zn2+

Hydrolysis

R

O

O

H2NO

O

S1' pocket

NH2

H2N

145

Inhibition of carboxypeptidase


No hydrolysisL-benzylsuccinic acid

OO

O

O

Zn2+

S1' pocket

NH2

H2N

145

Lead compounds for ACE inhibitor


Teprotide

Glu-Trp-Pro-Arg-Pro-Gln-Ile-Pro-Pro

L-Benzylsuccinic acid

OH

O

O

OH

N

O

HO

O

CO2H

Succinyl proline

Proposed binding mode


Succinyl prolineN

O

O

O

CO2

Zn2+

H2N

H2N

S1' pocket

S1 pocket

Extension and bio-isostere strategies


N

O

HS

CO2

CH3

S1' pocket

S1 pocket

Zn2+

H2N

H2N

N

O

O

OH

CO2H

N

O

O

OH

CO2H

CH3

N

O

HS

CO2H

CH3

Captopril

Extension strategies


Inhibitor

NH

N

O CO2

O

O

CH3

S1' pocket

S1 pocket

Zn2+

H2N

H2N

NHN

O CO2H

O

O

NH

N

O CO2H

O

O

CH3

Enalaprilate

NH

N

O CO2H

O

O

CH3

Computer-Assisted Drug Design (CADD)

1. Direct design of active substances which can be envisaged when the 3D structure of the target molecule is known. In this case the macromolecule can be built with the aid of computer then the fit of the host molecule with its receptor can be optimized. The structure of the ligand, its substituents and confirmation can be modified and the most favorable conditions for interaction (docking) can be simulated on the screen.

In practice molecular modeling uses two approaches:

gDock: Web Docking Tool

Sketch Structure Docked Structure

2. Indirect design of active substances, on the other hand, constitutes the only possible approach when the 3D structure of the target molecule is unknown. In this situation comparison of a set of ligands selective for a given receptor is undertaken in order to reveal the molecular information that the compounds have in common despite apparently different chemical formula.

5.24.2-4.7

6.7

4.8

5.1-7.1

5.24.2-4.7

6.7

4.8

5.1-7.1

8 .Pharmacokinetics – drug design

Aims

• To improve pharmacokinetic properties of lead compound

• To optimise chemical and metabolic stability (stomach acids / digestive enzymes / metabolic

enzymes)

• To optimise hydrophilic / hydrophobic balance (solubility in blood / solubility in GIT / solubility

through cell membranes / access to CNS / excretion rate)

• Drugs must be polar - to be soluble in aqueous conditions - to interact with molecular

targets

• Drugs must be ‘lipophilic’ - to cross cell membranes - to avoid rapid

excretion

• Drugs must have both hydrophilic and lipophilic characteristics

• Many drugs are weak bases with pKa’s 6-8

Receptor interaction& water solubility

Crossesmembranes

+ H

HN N H

H

- H

8 .Pharmacokinetics – drug design

Rationale:• Metabolism of drugs usually occurs at specific sites. Introduce

groups at a susceptible site to block the reaction• Increases metabolic stability and drug lifetime

Oral contraceptive - limited lifetime

8.1.1 Metabolic blockers

MetabolicOxidation

6 MegestrolAcetate

CO

C

H

O

Me

Me

H H

Me OMe

O

MetabolismBlocked

6

Me

Me

O

Me

CO C

H

H H

Me O Me

O

8.1 Drug stability

Rationale:• Metabolism of drugs usually occurs at specific groups. • Remove susceptible group or replace it with metabolically

stable group [e.g. modification of tolbutamide (oral hypoglycemic)]

Susceptible group

Unsusceptible group

8.1.2 Remove / replace susceptible metabolic groups

Metabolism

TOLBUTAMIDE

Me S

O

O

NH C

O

NH CH2CH2CH2CH3 NH CH2CH2CH3C

O

NHS

O

O

Cl

Rapidly excreted - short lifetime

Metabolism

HOOC S

O

O

NH C

O

NH CH2CH2CH2CH3

Rationale:• Used if the metabolically susceptible group is important for binding• Shift its position to make it unrecognisable to metabolic enzyme • Must still be recognisable to targetExample:

SalbutamolSusceptible

group

Unsusceptible group

8.1.3 Shifting susceptible metabolic groups

CatecholO-MethylTransferase

ShiftGroup

Salbutamol

HO C

OH

OH

CH2 NH C

Me

Me

Me

H

C

Me

Me

Me

NHCHCH2

HO

OH

HO

CatecholO-MethylTransferase

HO CHCH2

OH

MeO

NH C

Me

Me

Me

Inactive

Rationale:• Drug ‘smuggled’ into cell by carrier proteins for natural building

block (e.g. amino acids or nucleic acid bases)• Increases selectivity of drugs to target cells and reduces toxicity to

other cells

Example: Anticancer drugs

• Alkylating group is attached to a nucleic acid base• Cancer cells grow faster than normal cells and have a greater

demand for nucleic acid bases• Drug is concentrated in cancer cells - Trojan horse tactic

8.3.1 Linking a biosynthetic building block

8.3 Drug targeting

Non selective alkylating agentToxic

N

Cl

Cl

H3C

Uracil Mustard

HN

HN

O

O

N

Cl

Cl

Rationale:• Toxicity is often due to specific functional groups• Remove or replace functional groups known to be toxic e.g.

- aromatic nitro groups- aromatic amines- bromoarenes- hydrazines- polyhalogenated groups- hydroxylamines

• Vary substituents• Vary position of substituents

9. Reducing drug toxicity

Definition:Inactive compounds which are converted to active compounds in

the body.

Uses: • Improving membrane permeability• Prolonging activity• Masking toxicity and side effects• Varying water solubility• Drug targeting• Improving chemical stability

9.1 Prodrugs

Example:Aspirin for salicylic acid

9.1.2 Prodrugs to mask toxicity and side effects• Mask groups responsible for toxicity/side effects• Used when groups are important for activity

Salicylic acid• Analgesic, but causes stomachulcers due to phenol group

Aspirin• Phenol masked by ester• Hydrolysed in body

OH

CO2H O

CO2H

O

H3C

Example: Cyclophosphoramide for phosphoramide mustard

)anticancer agent(

9.1.2 Prodrugs to mask toxicity and side effects

Cyclophosphoramide•Non toxic•Orally active

Phosphoramide mustard• Alkylating agent

Phosphoramidase)liver(

O

P

NH O

N

Cl

Cl

HO

P

Cl

Cl

N

OH2N

9.1.3 Prodrugs to enhance patient acceptability• Used to reduce solubility of foul tasting orally active drugs • Less soluble on tongue• Less revolting taste

Example:Palmitate ester of chloramphenicol (antibiotic)

Palmitate ester

O2N

OH

HN

O

O

Cl

ClH

H

O Esterase

Chloramphenicol

O2N

OH

HN

O

OH

Cl

ClH

H

9.1.4 Prodrugs to increase water solubility• Often used for i.v. drugs • Allows higher concentration and smaller dose volume• May decrease pain at site of injection

Example:Succinate ester of chloramphenicol (antibiotic)

Succinate ester

O2N

OH

HN

O

O

Cl

ClH

H

O

OHO

Esterase

Chloramphenicol

O2N

OH

HN

O

OH

Cl

ClH

H

Drug MetabolismIdentification of drug metabolites in test animals

Properties of drug metabolites

ToxicologyIn vivo and in vitro tests for acute and chronic toxicity

PharmacologySelectivity of action at drug target

FormulationStability testsMethods of delivery

Preclinical trials

Phase I trials

• first introduction of IND (investigational new drug) in

humans

• usually only healthy adult volunteers (no patients)

• purpose is to investigate metabolic and pharmacological

actions of the compound in humans

• use dose-ranging (increasing dosages) to determine what

side effects may occur

• usually 20 – 80 subjects in the trial

Phase II trials

• early controlled trials in a patient population, with limited

scope, to obtain preliminary data on efficacy

• further indication of side effects, this time in patients

• about 200-400 subjects

Phase III trials

• expanded trials in a much larger sample of

patients

• more information about drug efficacy and safety

• information about benefit : risk ratio

• obtain some information to determine what

should be included in the labelling of the

marketed drug

• several hundred to several thousand patient

subjects (usually multi-centre studies and very

expensive)

Phase IV trials

• not always performed

• may be required to explore possible side effects in more detail

or give a better indication of efficacy

• may involve a different type of patient (different age range,

different male:female ratio)

• may investigate potential efficacy in a different therapeutic

area

• number of subjects is variable depending upon the reason for

the study

Drug Discovery ProcessTime and Money

Drug Discovery ProcessTime and Money

12 to 24 years

1 drug

50,000 - 5,000,000 compounds areoften screened to find a single drug

$300 to >$500 million

>1,000“ hits”

12“ leads”

6 drug candidates

Discovery & Preclinical trials Clinical trials: Phase I, Phase II, Phase III

Epidemiology• Distribution, frequency and determinants of health

problems and diseases in human populations• Aim: obtain, interpret and use health information and

reduce disease burden• Practical interventions and programs

Components:

1- Disease Frequency: Rates and Ratios. 2- Disease Distribution:Patterns of the disease distribution.3- Disease Determinants: To identify underlying causes.

Concepts and their application • Incidence: the number of new cases, episodes or

events occurring over a defined period of time, commonly one year.

• Prevalence: the total number of existing cases, episodes or events occurring at one point in time, commonly on a particular day.

• Population at risk: is vital to know about all people at risk of developing a disease or having a health problem, as well as those who are currently suffering from it.

Uses of epidemiology• Study effects of disease states in populations over

time and predict future health needs• Diagnose the health of the community• Evaluate health services• Estimate individual risk from group experience• Identify syndromes• Complete the clinical picture so that prevention

can be accomplished before disease is irreversible

• Search for cause

Pharmacogenetics

The term pharmacogenetics comes from the combination of two words:

• Pharmacogenetics– Study of how genetic differences in a SINGLE

gene influence variability in drug response (i.e., efficacy and toxicity)

• Pharmacogenomics– Study of how genetic (genome) differences in

MULTIPLE genes influence variability in drug response (i.e., efficacy and toxicity)

AIM OF PHARMACOGENETIC STUDIES AIM OF PHARMACOGENETIC STUDIES

Identify and categorize the genetic factors that underlie the differences and apply this in clinical practice

Rational, individual therapy Screening for those patients who carry the genes

which place them at risk in case of certain therapiesDiscovering which drugs are potentially dangerous

for carriers of a given polymorphismEstablishing the frequency of pharmacogenetic

phenotypes

Non-responders and toxic responders

Responders treat with

convential drugs

GENETIC FACTORS: The first observations of genetic variation in drug response date from the 1950’s, involving the muscle relaxant suxamethonium chloride. One in 3500 Caucasians has less efficient variant of the enzyme (butyrylcholinesterase) that metabolizes suxamethonium chloride. As a consequence, the drug’s effect is prolonged, with slower recovery from surgical paralysis.

53

A. Atypical Plasma Cholinesterase

•a rapid acting, rapid recovery muscle relaxant - 1951•usual paralysis lasted 2 to 6 min in patients•occasional patient exhibited paralysis lasting hrs.•cause identified as an “atypical” plasma cholinesterase

Hydrolysis by pseudocholinesterase

choline succinylmonocholine

O C CH2CH2

O

(H3C)3NH2CH2C C

O

O CH2CH2N(CH3)3+ +

SUCCINYLCHOLINE

Potential Benefits of Pharmacogenetics Improve Drug Choices:• Each year, many dies of adverse reactions to medicine.• Pharmacogenomics will predict who's likely to have a negative or

positive reaction to a drug Safer Dosing Options• Testing of Genomic Variation Improve Determination of Correct

Dose for Each Individual Improvement in Drug Development:• Permit pharmaceutical companies to determine in which

populations new drugs will be effective Decrease Health Care Costs• Reduce number of deaths & hospitalizations due to adverse drug

reactions. Reduce purchase of drugs which are ineffective in certain individuals due to genetic variations

Speed Up Clinical Trials for New Drugs

Rationale : Endogenous lead compounds often simple and flexible (e.g. adrenaline)Endogenous lead...

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