Optimizing Target Interactions. Stages of drug design and development 1) Identify target disease 2) Identify drug target 3) Establish testing procedures

Optimizing Target Interactions

Stages of drug design and developmentStages of drug design and development

1) Identify target disease 2) Identify drug target 3) Establish testing procedures 4) Find a lead compound 5) Structure-activity relationships (SAR) 6) Identify a pharmacophore 7) Drug design - optimizing target interactions 8) Drug design - optimizing pharmacokinetic properties 9) Toxicological and safety tests10) Chemical development and production11) Patenting and regulatory affairs12) Clinical trials

Structure-activity relationships (SAR)Structure-activity relationships (SAR)

• Alter, remove or mask a functional group

• Test the analogue for activity

• Conclusions depend on the method of testing•in vitro - tests for binding interactions with target•in vivo - tests for target binding interactions and/or pharmacokinetics

• If in vitro activity drops, it implies group is important for binding

• If in vivo activity unaffected, it implies group is not important

Aim - Aim - Identify which functional groups are important for binding and/or activity

MethodMethod

• Modifications may disrupt binding by electronic / steric effects

• Easiest analogues to make are those made from lead compound

• Possible modifications may depend on other groups present

• Some analogues may have to be made by a full synthesis(e.g. replacing an aromatic ring with a cyclohexane ring)

• Allows identification of important groups involved in binding

• Allows identification of the pharmacophore


O

NMe

HO

HO

MORPHINEMORPHINE


O

NMe

H3CO

HO

CODEINECODEINE

ACTIVITY DROPSACTIVITY DROPS


O

NMe

HO

HO

MORPHINEMORPHINE


O

NMe

HO

O

6-OXYMORPHINE6-OXYMORPHINE

ACTIVITY UNAFFECTEDACTIVITY UNAFFECTED


O

NMe

HO

HO

MORPHINEMORPHINE

Important groups for activityStructure-activity relationships (SAR)Structure-activity relationships (SAR)

HBD

SAR on alcoholsSAR on alcohols

Possible binding interactionsPossible binding interactions

Possible analoguesPossible analogues

X

Binding site

X= N or O

OH

Drug

O

H

Drug

X

Binding site

H

HBA

R OH R OMeCH3I

CH3COClR

O

O

CH3

CH3SO2Cl

R SO

O

CH3

O

LiAlH4R H

EtherEther

EsterEster

AlkaneAlkane

Possible effect of analogues on bindingPossible effect of analogues on binding(e.g. ether)(e.g. ether)

X

Binding site

X= N or OX

Binding site

H

No interaction as HBD No interaction as HBA

steric shield

OCH3

Ether analogue

OCH3

Ether analogue

SAR on alcoholsSAR on alcohols

Possible binding interactions if amine is ionizedPossible binding interactions if amine is ionized

SAR on 1SAR on 1oo, 2, 2oo & 3 & 3oo amines amines (RNH(RNH22, RNHR, R, RNHR, R33N)N)

IonicIonic

H-BondingH-Bonding

HBD

X

Binding site

X= N or O

CO2-

Binding site

NH2R

Drug

+

NH

Drug

R2

+RR33NNHH acts as a acts as a strong HBDstrong HBD

+

Possible binding interactions for free basePossible binding interactions for free base

H-BondingH-Bonding

HBD

X

Binding site

X= N or OX

Binding site

H

HBA

NH

Drug

RN

R

Drug

H

Note: Note: 3o Amines are only able to act as HBA’s - no hydrogen available to act as HBD


Analogues ofAnalogues of11oo & 2 & 2oo amines amines

Effect on bindingEffect on binding

CO2-

Binding site

No interaction

N CH3

O

R

Amide analogue

NotesNotes• 1o and 2o amines are converted to 2o and 3o amides respectively• Amides cannot ionize and so ionic bonding is not possible• An amide N is a poor HBA and so this eliminates HBA interactions• Steric effect of acyl group is likely to hinder NH acting as a HBD (2o amide)

R NH2

CH3COCl

R

HN

O

CH3


Analogues of 3Analogues of 3oo amines containing a methyl substituent amines containing a methyl substituent

R NHRCH3COCl

R

RN

O

CH3R NHR

CH3

VOC-Cl

O CH3

O

Demethylation

2o amine

3o amide



AnaloguesAnalogues Full synthesis of 1o-3o amines and amides

SAR on quaternary ammonium salts SAR on quaternary ammonium salts (R(R44NN++))

CO2-

Binding site

Ionicbonding

NR3

Drug

+

NR3

Drug

+

Induceddipole interactions

Binding site

+-


AnaloguesAnalogues

SAR on aldehydes and ketonesSAR on aldehydes and ketones

Dipole-dipoleinteraction

Binding site (X= N or O)

XH

H-BondingHBA

O

Drug

Binding site

O

Drug

R R'

ONaBH4 or LiAlH4

R R'

HO H

KetonePlanar sp2

carbon centre

2o AlcoholTetrahedral sp3

carbon centre

Effect on bindingEffect on binding

Change in stereochemistry (planar to tetrahedral)May move oxygen out of range

If still active, further reactions can be carried out on alcohol to establish importance of oxygen


X

HH

OH

Alcoholanalogue

SAR on aldehydes and ketonesSAR on aldehydes and ketones

Possible binding interactionsPossible binding interactions H-bonding as HBA by either oxygenH-bonding as HBA by either oxygen

AnaloguesAnalogues

NotesNotes• Hydrolysis splits molecule and may lead to a loss of activity due to loss of other functional groups - only suitable for simple esters.

• Hydrolysis leads to a dramatic increase in polarity which may influence ability of analogue to reach target if in vivo tests are used

• Reduction to alcohol removes carbonyl group and can establish importance of the carbonyl oxygen, but reaction can be difficult to do if other reactive functional groups are present

SAR on estersSAR on esters

RC

O

O

CH3

LiAlH4

NaOH RC

OH

O

CH3HO

RCH2

OH

+

Carboxylic acid Alcohol

1o Alcohol

NotesNotes• Esters are usually hydrolysed by esterases in the blood• Esters are more likely to be important for pharmacokinetic reasons i.e. acting as prodrugs

Ester masks polar groupsAllows passage throughfatty cell membranes

CO

O

R

ProdrugProdrug

OC

R

OProdrugProdrug

Fatty Fatty BarrierBarrier

CO

O

R

OC

R

O

COH

O

EsteraseEsteraseDrugDrug

OH

EsteraseEsteraseDrugDrug

SAR on estersSAR on esters


NotesNotes• The nitrogen of an amide cannot act as a HBA - lone pair interacts with neighboring carbonyl group• Tertiary amides unable to act as HBD’s

SAR on amidesSAR on amides


XH


X

HBAHBDN

Drug

H

O

RN

Drug

H

O

R

AnaloguesAnalogues

NotesNotes• Hydrolysis splits molecule and may lead to loss of activity due to loss of other functional groups - only suitable for simple amides.

• Hydrolysis leads to dramatic increase in polarity which may affect ability of analogue to reach target if in vivo tests are done

• Reduction to amine removes carbonyl group and can establish importance of the carbonyl oxygen, but reaction may be difficult to do if other reactive groups are present

SAR on amidesSAR on amides R

C

HN

O

R'

LiAlH4

NaOH RC

OH

O

R'H2N

RCH2

NH2

+

NaH / MeIR

C

CH3N

O

R'

Carboxylic acid Amine

1o Amine

3o Amide

SAR on amidesSAR on amides

• N-Methylation prevents HBD interaction and may introduce a steric effect that prevents an HBA interaction

No binding as HBD

X

N

CH3

O

R

Analogue

binding site

Binding of O as HBA hindered

XH

N

CH3

R

O

steric shield

Analogue

AnaloguesAnalogues

Possible binding interactions as free acidPossible binding interactions as free acid

SAR on carboxylic acidsSAR on carboxylic acids


XHHBA


XH

HBAC

OH

Drug

O

C

OH

Drug

O


X

HC

O

Drug

O

HBD

Possible binding interactions as carboxylate ionPossible binding interactions as carboxylate ion



XHHBA


NHR2+

Ionic bonding

OC

O

Drug

-

OC

O

Drug

-

NotesNotes• Charged oxygen atoms are strong HBA’s• Group can interact by ionic and hydrogen bonding at the same time

Possible analoguesPossible analogues

Possible effectsPossible effects• Reduction removes carbonyl oxygen as potential HBA and prevents ionization• Esterification prevents ionization, HBD interactions and may hinder HBA by a steric effect


No ionic bonding possible

NHR2

binding site

C

O

O

Analogue

CH3

+

H-Bonding hindered

XH

steric shield

C

O

O

Analogue

CH3

RC

OH

O

LiAlH4

H+ / R'OH RC

OR'

O

RCH2

OH

Ester

1o Alcohol

Possible effects on bindingPossible effects on binding

binding sitehydrophobichydrophobicregionregion

binding site

hydrophobichydrophobicpocketpocket

Analogue

HH

Nofit

Analogue

R RHH

‘Buffers’

SAR on aromatic rings and alkenesSAR on aromatic rings and alkenes

• Acid chlorides - too reactive to be of use• Acid anhydrides - too reactive to be of use

• Alkyl halides - present in anticancer drugs -react with nucleophiles in DNA• Aryl halides - commonly present. Not usually involved in binding directly• Nitro groups - sometimes present but often toxic• Alkynes - sometimes present, but not usually important in binding interactions• Thiols - present in some drugs as important binding group to transition metals (e.g. Zn in zinc metalloproteinases)• Nitriles - present in some drugs but rarely involved in binding

Notes• Functional groups may be important for electronic reasons

(e.g. nitro, cyano, aryl halides)• Functional groups may be important for steric reasons

(e.g. alkynes)

Miscellaneous functional groups in drugsMiscellaneous functional groups in drugs

Possible interactionsPossible interactions

SAR of alkyl groupsSAR of alkyl groups

hydrophobic slothydrophobic slot

binding site

Drug

CH3

van der Waalsinteractions

binding site

hydrophobic ‘pocket’hydrophobic ‘pocket’

Drug

CH3CH3

H3C

AnaloguesAnalogues Easiest alkyl groups to vary are substituents on heteroatomsVary length and bulk of alkyl group to test space available

SAR of alkyl groupsSAR of alkyl groups

N CH3

VOC-ClN H

R'XN R'

HBr R'X

O

CH3O

HO

R'

Hydrolysis R'OH

C

OCH3C

OH

O O H

C

OR'

O

Drug

Drug

Drug

Analogue

Analogue

Analogue

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Optimizing Target Interactions. Stages of drug design and development 1) Identify target disease 2) Identify drug target 3) Establish testing procedures