1 © patrick an introduction to medicinal chemistry 3/e chapter 13 quantitative structure- activity...

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Patrick Patrick An Introduction to Medicinal An Introduction to Medicinal

ChemistryChemistry 3/e 3/e

Chapter 13Chapter 13

QUANTITATIVE STRUCTURE-QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS ACTIVITY RELATIONSHIPS

(QSAR)(QSAR)

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ContentsContents

1. Introduction2. Hydrophobicity of the Molecule (4 slides)3. Hydrophobicity of Substituents (2 slides)4. Electronic Effects

4.1. Hammett Substituent Constant (s) (7 slides)

4.2. Electronic Factors R & F4.3. Aliphatic electronic substituents

5. Steric Factors (3 slides)6. Hansch Equation (4 slides)7. Craig Plot (2 slides)8. Topliss Scheme (5 slides)9. Bio-isosteres10. Free-Wilson Approach (3 slides)11. Case Study (10 slides)12. 3D-QSAR (10 slides)13. 3D-QSAR Case Study(7 slides)

[62 slides]

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1. Introduction1. Introduction

• AimsAims• To relate the biological activity of a series of compounds to To relate the biological activity of a series of compounds to

their physicochemical parameters in a quantitative fashion their physicochemical parameters in a quantitative fashion using a mathematical formulausing a mathematical formula

• RequirementsRequirements• Quantitative measurements for biological and Quantitative measurements for biological and

physicochemical propertiesphysicochemical properties

• Physicochemical PropertiesPhysicochemical Properties• Hydrophobicity of the moleculeHydrophobicity of the molecule• Hydrophobicity of substituentsHydrophobicity of substituents• Electronic properties of substituentsElectronic properties of substituents• Steric properties of substituentsSteric properties of substituents

Most commonMost commonproperties studiedproperties studied

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2. Hydrophobicity of the Molecule2. Hydrophobicity of the Molecule

Partition Coefficient Partition Coefficient PP = = [Drug[Drug in octanol]in octanol][Drug in water][Drug in water]

High High PP High hydrophobicity High hydrophobicity

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• Activity of drugs is often related to Activity of drugs is often related to PPe.g. binding of drugs to serum albumin e.g. binding of drugs to serum albumin (straight line - limited range of log (straight line - limited range of log PP))

• Binding increases as log Binding increases as log PP increases increases• Binding is greater for hydrophobic drugsBinding is greater for hydrophobic drugs

LogLog 11CC

0.75 log0.75 logPP ++ 2.302.30


Log (1/C)

Log P

. ..

.. .. ..

0.78 3.82

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Example 2Example 2 General anaesthetic activity of ethers General anaesthetic activity of ethers(parabolic curve - larger range of log (parabolic curve - larger range of log PP values) values)

Optimum value of log Optimum value of log PP for anaesthetic activity = log for anaesthetic activity = log PPoo

LogLog 11CC

-- 0.22(log0.22(logPP))22 ++ 1.04 log1.04 logPP ++ 2.162.16


Log PoLog P

Log (1/C)

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• QSAR equations are only applicable to compounds in the QSAR equations are only applicable to compounds in the same structural class (e.g. ethers)same structural class (e.g. ethers)

• However, log However, log PPoo is similar for anaesthetics of different is similar for anaesthetics of different structural classes (ca. 2.3)structural classes (ca. 2.3)

• Structures with log Structures with log PP ca. 2.3 enter the CNS easily ca. 2.3 enter the CNS easily(e.g. potent barbiturates have a log (e.g. potent barbiturates have a log PP of approximately 2.0) of approximately 2.0)

• Can alter log Can alter log PP value of drugs away from 2.0 to avoid CNS value of drugs away from 2.0 to avoid CNS side effectsside effects


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3. Hydrophobicity of Substituents3. Hydrophobicity of Substituents- the substituent hydrophobicity constant (p)- the substituent hydrophobicity constant (p)

• A measure of a substituent’s hydrophobicity relative to A measure of a substituent’s hydrophobicity relative to hydrogenhydrogen

• Tabulated values exist for aliphatic and aromatic substituentsTabulated values exist for aliphatic and aromatic substituents• Measured experimentally by comparison of log Measured experimentally by comparison of log P’sP’s with parent with parent

structurestructure

Example Example ::

• Positive values imply substituents are more hydrophobic than HPositive values imply substituents are more hydrophobic than H• Negative values imply substituents are less Negative values imply substituents are less

hydrophobic than Hhydrophobic than H

BenzeneBenzene(Log (Log PP = 2.13)= 2.13)

ChlorobenzeneChlorobenzene(Log (Log PP = 2.84)= 2.84)

BenzamideBenzamide(Log (Log PP = 0.64)= 0.64)

Cl CONH2

ClCl = 0.71 = 0.71 CONH CONH = -1.49 = -1.4922

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• The value ofThe value of is only valid for parent structures is only valid for parent structures• It is possible to calculate log It is possible to calculate log PP using using values values

• A QSAR equation may include both A QSAR equation may include both PP and and . . • PP measures the importance of a molecule’s overall measures the importance of a molecule’s overall

hydrophobicity hydrophobicity (relevant to absorption, binding etc)(relevant to absorption, binding etc)• identifies specific regions of the molecule which might identifies specific regions of the molecule which might

interact with hydrophobic regions in the binding siteinteract with hydrophobic regions in the binding site

3. Hydrophobicity of Substituents3. Hydrophobicity of Substituents- the substituent hydrophobicity constant (p)- the substituent hydrophobicity constant (p)

Example Example ::

metameta-Chlorobenzamide-Chlorobenzamide

Cl

CONH2

Log Log PP(theory)(theory) = log = log PP(benzene)(benzene) + + ClCl + + CONHCONH

= 2.13 + 0.71 - 1.49= 2.13 + 0.71 - 1.49 = 1.35= 1.35

Log Log PP (observed)(observed) = 1.51= 1.51

22

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4. Electronic Effects 4. Electronic Effects 4.1 Hammett Substituent Constant (s)4.1 Hammett Substituent Constant (s)

• The constant (The constant () a measure of the e-withdrawing or e-) a measure of the e-withdrawing or e-donating influence of substituentsdonating influence of substituents

• It can be measured experimentally and tabulated It can be measured experimentally and tabulated (e.g. (e.g. for aromatic substituents is measured by comparing the for aromatic substituents is measured by comparing the dissociation constants of substituted benzoic acids with benzoic acid)dissociation constants of substituted benzoic acids with benzoic acid)

X=HX=H KKHH == Dissociation constant Dissociation constant == [PhCO[PhCO22--]][PhCO[PhCO22H]H]

+CO2H CO2 H

X X

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+

X = electron withdrawing group

X

CO2CO2H

X

H

X= electron withdrawing group (e.g. NOX= electron withdrawing group (e.g. NO22))

XX == log log KKXX

KKHH == logKlogKXX -- logKlogKHH

Charge is stabilised by XCharge is stabilised by XEquilibrium shifts to rightEquilibrium shifts to rightKKXX > K > KHH

Positive valuePositive value

4.1 Hammett Substituent Constant (s)4.1 Hammett Substituent Constant (s)

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X= electron donating group (e.g. CHX= electron donating group (e.g. CH33))

XX == log log KKXX

KKHH == logKlogKXX -- logKlogKHH

Charge destabilisedCharge destabilisedEquilibrium shifts to leftEquilibrium shifts to leftKKXX < K < KHH

Negative valueNegative value


+

X = electron withdrawing group

X

CO2CO2H

X

H

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value depends on inductive and resonance effectsvalue depends on inductive and resonance effects

value depends on whether the substituent is value depends on whether the substituent is metameta or or parapara

orthoortho values are invalid due to steric factors values are invalid due to steric factors


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DRUG

N

O

O

metameta-Substitution-Substitution

EXAMPLES:EXAMPLES: pp (NO (NO22)) mm (NO (NO22))

e-withdrawing (inductive effect only)e-withdrawing (inductive effect only)

e-withdrawing e-withdrawing (inductive + (inductive + resonance effects)resonance effects)


NO O

DRUG DRUG

NOO

NO O

DRUG DRUG

NOO

parapara-Substitution-Substitution

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mm (OH) (OH) pp (OH) (OH)

e-withdrawing (inductive effect only)e-withdrawing (inductive effect only)

e-donating by resonance e-donating by resonance more important than more important than inductive effectinductive effect


EXAMPLES:EXAMPLES:

DRUG

OH

metameta-Substitution-Substitution

DRUG

OH

DRUG DRUG

OH OH

DRUG

OH

parapara-Substitution-Substitution

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QSAR Equation:QSAR Equation:

DiethylphenylphosphatesDiethylphenylphosphates(Insecticides)(Insecticides)

loglog 11CC

2.2822.282 -- 0.3480.348

Conclusion :Conclusion : e-withdrawing substituents increase activity e-withdrawing substituents increase activity


XO P

O

OEt

OEt

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4.2 Electronic Factors 4.2 Electronic Factors RR & & FF

• RR - Quantifies a substituent’s resonance effects - Quantifies a substituent’s resonance effects

• FF - Quantifies a substituent’s inductive effects - Quantifies a substituent’s inductive effects

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4.3 Aliphatic electronic substituents4.3 Aliphatic electronic substituents • Defined by Defined by II

• Purely inductive effectsPurely inductive effects• Obtained experimentally by measuring the rates of hydrolyses Obtained experimentally by measuring the rates of hydrolyses

of aliphatic estersof aliphatic esters• Hydrolysis rates measured under basic and acidic conditionsHydrolysis rates measured under basic and acidic conditions

X= electron donatingX= electron donating RateRate I I = -ve= -ve

X= electron withdrawingX= electron withdrawing RateRate I I = +ve= +ve

Basic conditions: Basic conditions: Rate affected by steric + electronic factorsRate affected by steric + electronic factorsGives Gives II after correction for steric effect after correction for steric effect

Acidic conditions: Acidic conditions: Rate affected by steric factors only (see Rate affected by steric factors only (see EEss))

+Hydrolysis

HOMeCH2 OMe

C

O

X CH2 OHC

O

X

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5. Steric Factors5. Steric Factors Taft’s Steric Factor (Taft’s Steric Factor (EEss))

• Measured by comparing the rates of hydrolysis of substituted Measured by comparing the rates of hydrolysis of substituted aliphatic esters against a standard ester under acidic aliphatic esters against a standard ester under acidic conditionsconditions

EEss = log = log kkxx - log - log kkoo kkxx represents the rate of hydrolysis of a substituted ester represents the rate of hydrolysis of a substituted ester

kkoo represents the rate of hydrolysis of the parent represents the rate of hydrolysis of the parent

esterester

• Limited to substituents which interact sterically with the Limited to substituents which interact sterically with the tetrahedral transition state for the reactiontetrahedral transition state for the reaction

• Cannot be used for substituents which interact with the Cannot be used for substituents which interact with the transition state by resonance or hydrogen bondingtransition state by resonance or hydrogen bonding

• May undervalue the steric effect of groups in an May undervalue the steric effect of groups in an intermolecular process (i.e. a drug binding to a receptor)intermolecular process (i.e. a drug binding to a receptor)

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5. Steric Factors5. Steric Factors Molar Refractivity (Molar Refractivity (MRMR)) - a measure of a substituent’s volume - a measure of a substituent’s volume

MRMR == (n(n 22 -- 1)1)

(n(n 22 -- 2)2) x x

mol. wt.mol. wt.

densitydensity

Correction factor Correction factor for polarisationfor polarisation

(n=index of (n=index of refraction)refraction)

Defines volumeDefines volume

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5. Steric Factors5. Steric Factors Verloop Steric ParameterVerloop Steric Parameter

- calculated by software (STERIMOL)- calculated by software (STERIMOL)- gives dimensions of a substituent- gives dimensions of a substituent

- can be used for any substituent- can be used for any substituent

L

B3

B4

B4 B3

B2

B1

C

O

O

H

H O C O

Example - Carboxylic acidExample - Carboxylic acid

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6. Hansch Equation6. Hansch Equation

• A QSAR equation relating various physicochemical properties A QSAR equation relating various physicochemical properties to the biological activity of a series of compoundsto the biological activity of a series of compounds

• Usually includes log Usually includes log PP, electronic and steric factors, electronic and steric factors

• Start with simple equations and elaborate as more structures Start with simple equations and elaborate as more structures are synthesisedare synthesised

• Typical equation for a wide range of log Typical equation for a wide range of log PP is parabolic is parabolic

LogLog 11CC

-- k (logk (logPP))22 ++ kk 22 loglogPP ++ kk 33 ++ kk 44 EEss ++ kk 5511

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LogLog 11CC

1.22 1.22 -- 1.59 1.59 ++ 7.897.89

Conclusions:Conclusions:• Activity increases if Activity increases if is +ve (i.e. hydrophobic substituents) is +ve (i.e. hydrophobic substituents)• Activity increases if Activity increases if is negative (i.e. e-donating substituents) is negative (i.e. e-donating substituents)

Example: Example: Adrenergic blocking activity of Adrenergic blocking activity of -halo--halo--arylamines-arylamines

CH CH2 NRR'

XY

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Conclusions:Conclusions:• Activity increases slightly as log Activity increases slightly as log PP (hydrophobicity) increases (hydrophobicity) increases

(note that the constant is only 0.14)(note that the constant is only 0.14)• Parabolic equation implies an optimum log Parabolic equation implies an optimum log PPoo value for activity value for activity• Activity increases for hydrophobic substituents (esp. ring Y)Activity increases for hydrophobic substituents (esp. ring Y)• Activity increases for e-withdrawing substituents (esp. ring Y)Activity increases for e-withdrawing substituents (esp. ring Y)

LogLog 11CC

-- 0.015 (log0.015 (logPP))22 ++ 0.14 log0.14 logPP ++ 0.27 0.27 XX ++ 0.40 0.40 YY ++ 0.65 0.65 XX++ 0.88 0.88 YY ++ 2.342.34


Example: Example: Antimalarial activity of phenanthrene aminocarbinolsAntimalarial activity of phenanthrene aminocarbinols

X

Y

(HO)HC

CH2NHR'R"

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Substituents must be chosen to satisfy the following criteria:Substituents must be chosen to satisfy the following criteria:

• A range of values for each physicochemical property studiedA range of values for each physicochemical property studied• values must not be correlated for different properties (i.e. they values must not be correlated for different properties (i.e. they

must be orthogonal in value) must be orthogonal in value) • at least 5 structures are required for each parameter studiedat least 5 structures are required for each parameter studied

Correlated values. Correlated values. Are any differences Are any differences due to due to or MR? or MR?

No correlation in valuesNo correlation in valuesValid for analysing effectsValid for analysing effectsof of and MR. and MR.


Substituent H Me Et n-Pr n-BuSubstituent H Me Et n-Pr n-Bu 0.00 0.56 1.02 1.50 2.130.00 0.56 1.02 1.50 2.13MRMR 0.10 0.56 1.03 1.55 1.96 0.10 0.56 1.03 1.55 1.96

Substituent H Me OMe NHCONHSubstituent H Me OMe NHCONH22 I CN I CN

0.00 0.56 -0.02 -1.30 1.12 -0.570.00 0.56 -0.02 -1.30 1.12 -0.57MRMR 0.10 0.56 0.79 1.37 1.39 0.63 0.10 0.56 0.79 1.37 1.39 0.63

Choosing suitable substituentsChoosing suitable substituents

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7. Craig Plot7. Craig Plot Craig plot shows values for 2 different physicochemical properties Craig plot shows values for 2 different physicochemical properties for various substituentsfor various substituents

ExampleExample::

.

+

-

-.25

.75

.50

1.0

-1.0

-.75

-.50

.25

-.4-.8-1.2-1.6-2.0 2.01.61.2.8.4. . . .

...

.

.. . ..

..

.

......

CF3SO2

CF3

Me

Cl Br I

OCF3

F

NMe2

OCH3

OH

NH2

CH3CONH

CO2H

CH3CO

CN

NO2

CH3SO2

CONH2

SO2NH2

Ett-Butyl

SF5

- +

- +

+ +

- -

+ -

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• Allows an easy identification of suitable substituents for a Allows an easy identification of suitable substituents for a QSAR analysis which includes both relevant propertiesQSAR analysis which includes both relevant properties

• Choose a substituent from each quadrant to ensure Choose a substituent from each quadrant to ensure orthogonalityorthogonality

• Choose substituents with a range of values for each propertyChoose substituents with a range of values for each property

7. Craig Plot7. Craig Plot

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8. Topliss Scheme8. Topliss Scheme Used to decide which substituents to use if optimising compounds Used to decide which substituents to use if optimising compounds one by one (where synthesis is complex and slow)one by one (where synthesis is complex and slow)

Example: Aromatic substituentsExample: Aromatic substituents

L E M

ML EL E M

L E M

L E M

See CentralBranch

L E M

H

4-Cl

4-CH34-OMe 3,4-Cl2

4-But 3-CF3-4-Cl

3-Cl 3-Cl 4-CF3

2,4-Cl2

4-NO2

3-NMe2

3-CF3-4-NO2

3-CH3

2-Cl

4-NO2

3-CF3

3,5-Cl2

3-NO2

4-F

4-NMe2

3-Me-4-NMe2

4-NH2

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RationaleRationaleReplace H with Replace H with parapara-Cl (+-Cl (+ and + and +))

++ and/or + and/or +advantageousadvantageous

favourable favourable unfavourable unfavourable

++ and/or + and/or +disadvantageousdisadvantageous

ActAct.. LittleLittlechangechange

Act.Act.

add second Cl to add second Cl to increase increase and and furtherfurther

replace with OMereplace with OMe(-(- and - and -))

replace with Mereplace with Me(+(+ and - and -))

Further changes suggested based on arguments of Further changes suggested based on arguments of and and steric strainsteric strain

8. Topliss Scheme8. Topliss Scheme

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8. Topliss Scheme8. Topliss Scheme Aliphatic substituentsAliphatic substituents

L E M

L E L E MM

CH3

i-Pr

H; CH2OCH3 ; CH2SO2CH3 Et Cyclopentyl

END Cyclohexyl

CHCl2 ; CF3 ; CH2CF3 ; CH2SCH3

Ph ; CH2Ph

CH2Ph

CH2CH2Ph

Cyclobutyl; cyclopropyl

t-Bu

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8. Topliss Scheme8. Topliss Scheme ExampleExample

M= More ActivityL= Less ActivityE = Equal Activity

HighPotency

*

-MLEM

H4-Cl3,4-Cl24-Br4-NO2

12345

Biological Activity

ROrder ofSynthesis

R

SO2NH2

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8. Topliss Scheme8. Topliss Scheme ExampleExample

*

*

Order ofSynthesis

R Biological Activity

12345678

H4-Cl4-MeO3-Cl3-CF33-Br3-I3,5-Cl2

-LLMLMLM

*

HighPotency

M= More ActivityL= Less ActivityE = Equal Activity

R N N

N

CH2CH2CO2H

N

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9. Bio-isosteres9. Bio-isosteres

• Choose substituents with similar physicochemical properties Choose substituents with similar physicochemical properties ((e.g. CN, NOe.g. CN, NO22 and COMe could be bio-isosteres) and COMe could be bio-isosteres)

• Choose bio-isosteres based on most important Choose bio-isosteres based on most important physicochemical property physicochemical property (e.g. COMe & SOMe are similar in (e.g. COMe & SOMe are similar in pp; SOMe and SO; SOMe and SO22Me are similar in Me are similar in

))

-0.55-0.55 0.40 0.40 -1.58-1.58 -1.63-1.63 -1.82-1.82 -1.51-1.51pp 0.50 0.50 0.84 0.84 0.49 0.49 0.72 0.72 0.57 0.57 0.36 0.36

mm 0.38 0.38 0.66 0.66 0.52 0.52 0.60 0.60 0.46 0.46 0.35 0.35

MRMR 11.211.2 21.521.5 13.713.7 13.513.5 16.916.9 19.219.2

Substituent C

O

CH3

CCH3

CNC CN

SCH3

O

S

O

CH3

O

S

O

NHCH3

O

C

O

NMe2

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10. Free-Wilson Approach10. Free-Wilson Approach

• The biological activity of the parent structure is measured The biological activity of the parent structure is measured and compared with the activity of analogues bearing and compared with the activity of analogues bearing different substituentsdifferent substituents

• An equation is derived relating biological activity to the An equation is derived relating biological activity to the presence or absence of particular substituentspresence or absence of particular substituents

Activity = kActivity = k11XX11 + k + k22XX22 +.…k +.…knnXXnn + Z + Z

• XXnn is an is an indicator variableindicator variable which is given the value 0 or 1 which is given the value 0 or 1

depending on whether the substituent (n) is present or notdepending on whether the substituent (n) is present or not• The contribution of each substituent (n) to activity is The contribution of each substituent (n) to activity is

determined by the value of kdetermined by the value of knn

• Z is a constant representing the overall activity of the Z is a constant representing the overall activity of the structures studiedstructures studied

MethodMethod

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10. Free-Wilson Approach10. Free-Wilson Approach

• No need for physicochemical constants or tablesNo need for physicochemical constants or tables• Useful for structures with unusual substituentsUseful for structures with unusual substituents• Useful for quantifying the biological effects of molecular Useful for quantifying the biological effects of molecular

features that cannot be quantified or tabulated by the features that cannot be quantified or tabulated by the Hansch methodHansch method

AdvantagesAdvantages

DisadvantagesDisadvantages

• A large number of analogues need to be synthesised to A large number of analogues need to be synthesised to represent each different substituent and each different represent each different substituent and each different position of a substituentposition of a substituent

• It is difficult to rationalise why specific substituents are It is difficult to rationalise why specific substituents are good or bad for activitygood or bad for activity

• The effects of different substituents may not be additiveThe effects of different substituents may not be additive(e.g. intramolecular interactions)(e.g. intramolecular interactions)

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10. Free-Wilson / Hansch Approach10. Free-Wilson / Hansch Approach

• It is possible to use indicator variables as part of a Hansch It is possible to use indicator variables as part of a Hansch equation - see following Case Studyequation - see following Case Study

AdvantagesAdvantages

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11. Case Study11. Case Study QSAR analysis of pyranenamines (SK & F) QSAR analysis of pyranenamines (SK & F) (Anti-allergy compounds(Anti-allergy compounds))

O O O

NH

O OH OH X

Y

Z

3

4

5

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Stage 1Stage 1 19 structures were synthesised to study 19 structures were synthesised to study and and

CCLogLog11

-- 0.140.14 -- 1.35(1.35( ))22 0.720.72

and and = total values for = total values for and and for all substituents for all substituents

Conclusions:Conclusions: • Activity drops as Activity drops as increases increases• Hydrophobic substituents are bad for activity - unusualHydrophobic substituents are bad for activity - unusual• Any value of Any value of results in a drop in activity results in a drop in activity• Substituents should not be e-donating or e-withdrawing Substituents should not be e-donating or e-withdrawing

(activity falls if (activity falls if is +ve or -ve)is +ve or -ve)

11. Case Study11. Case Study O O O

NH

O OH OH X

Y

Z

3

4

5

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Stage 2Stage 2 61 structures were synthesised, concentrating on 61 structures were synthesised, concentrating on hydrophilic substituents to test the first equationhydrophilic substituents to test the first equation

AnomaliesAnomalies a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. Activity should drop as alkyl group becomes bigger and more Activity should drop as alkyl group becomes bigger and more hydrophobic, but the activity is similar for all three substituentshydrophobic, but the activity is similar for all three substituents

b) OH, SH, NHb) OH, SH, NH22 and NHCOR at position 5 : Activity is greater than expected and NHCOR at position 5 : Activity is greater than expected

c) NHSOc) NHSO22R : Activity is worse than expectedR : Activity is worse than expected

d) 3,5-(CFd) 3,5-(CF33))22 and 3,5(NHMe) and 3,5(NHMe)2 2 : Activity is greater than expected: Activity is greater than expected

e) 4-Acyloxy : Activity is 5 x greater than expectede) 4-Acyloxy : Activity is 5 x greater than expected


NH

O OH OH X

Y

Z

3

4

5

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a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. Possible steric factor at work. Increasing the size of R may be good for activity Possible steric factor at work. Increasing the size of R may be good for activity and balances out the detrimental effect of increasing hydrophobicityand balances out the detrimental effect of increasing hydrophobicity

b) OH, SH, NHb) OH, SH, NH22, and NHCOR at position 5, and NHCOR at position 5

Possibly involved in H-bondingPossibly involved in H-bonding

c) NHSOc) NHSO22R R

Exception to H-bonding theory - perhaps bad for steric or electronic reasonsException to H-bonding theory - perhaps bad for steric or electronic reasons

d) 3,5-(CFd) 3,5-(CF33))22 and 3,5-(NHMe) and 3,5-(NHMe)22

The only disubstituted structures where a substituent at position 5 was electron The only disubstituted structures where a substituent at position 5 was electron withdrawingwithdrawing

e) 4-Acyloxye) 4-AcyloxyPresumably acts as a prodrug allowing easier crossing of cell membranes.Presumably acts as a prodrug allowing easier crossing of cell membranes.The group is hydrolysed once across the membrane.The group is hydrolysed once across the membrane.


NH

O OH OH X

Y

Z

3

4

5TheoriesTheories

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Stage 3Stage 3 Alter the QSAR equation to take account of new results Alter the QSAR equation to take account of new results

LogLog 11CC

-- 0.300.30 -- 1.35(1.35( ))22 ++ 2.0(2.0(FF-- 5) 5) ++ 0.39(3450.39(345 --HBD) HBD) -- 0.63(NHSO0.63(NHSO22))

++ 0.78(0.78(MM -- VV) ) ++ 0.72(40.72(4-- OCO) OCO) -- 0.750.75ConclusionsConclusions((FF-5) -5) e-withdrawing group at position 5 increases activity e-withdrawing group at position 5 increases activity

(based on only 2 compounds though)(based on only 2 compounds though)(3,4,5-HBD) (3,4,5-HBD) H-bond donor group at positions 3, 4,or 5 is good for activityH-bond donor group at positions 3, 4,or 5 is good for activity Term = 1 if a HBD group is at any of these positionsTerm = 1 if a HBD group is at any of these positions

Term = 2 if HBD groups are at two of these positionsTerm = 2 if HBD groups are at two of these positions Term = 0 if no HBD group is present at these positionsTerm = 0 if no HBD group is present at these positions Each HBD group increases activity by 0.39Each HBD group increases activity by 0.39

(NHSO(NHSO22) ) Equals 1 if NHSOEquals 1 if NHSO22 is present (bad for activity by -0.63). is present (bad for activity by -0.63).

Equals zero if group is absent.Equals zero if group is absent.((M-VM-V) ) Volume of any Volume of any metameta substituent. Large substituents at substituent. Large substituents at metameta

position increase activityposition increase activity4-O-CO 4-O-CO Equals 1 if acyloxy group is present (activity increases by 0.72). Equals 1 if acyloxy group is present (activity increases by 0.72).

Equals 0 if group absentEquals 0 if group absent


NH

O OH OH X

Y

Z

3

4

5

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Stage 3Stage 3 Alter the QSAR equation to take account of new results Alter the QSAR equation to take account of new results

LogLog 11CC

-- 0.300.30 -- 1.35(1.35( ))22 ++ 2.0(2.0(FF-- 5) 5) ++ 0.39(3450.39(345 --HBD) HBD) -- 0.63(NHSO0.63(NHSO22))

++ 0.78(0.78(MM -- VV) ) ++ 0.72(40.72(4-- OCO) OCO) -- 0.750.75

The terms (3,4,5-HBD), (NHSOThe terms (3,4,5-HBD), (NHSO22), and 4-O-CO are examples of indicator ), and 4-O-CO are examples of indicator

variables used in the free-Wilson approach and included in a Hansch equation variables used in the free-Wilson approach and included in a Hansch equation


NH

O OH OH X

Y

Z

3

4

5

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Stage 4Stage 4 37 Structures were synthesised to test steric and 37 Structures were synthesised to test steric and FF-5 parameters, -5 parameters, as well as the effects of hydrophilic, H-bonding groupsas well as the effects of hydrophilic, H-bonding groups

AnomaliesAnomaliesTwo H-bonding groups are bad if they are Two H-bonding groups are bad if they are orthoortho to each other to each other

ExplanationExplanationPossibly groups at the Possibly groups at the orthoortho position bond with each other rather position bond with each other rather than with the receptor - an intramolecular interactionthan with the receptor - an intramolecular interaction


NH

O OH OH X

Y

Z

3

4

5

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Stage 5Stage 5 Revise Equation Revise Equation

a) Increasing the hydrophilicity of substituents allows the identification of an a) Increasing the hydrophilicity of substituents allows the identification of an optimum value for optimum value for ( ( = -5). The equation is now parabolic (-0.034 ( = -5). The equation is now parabolic (-0.034 ())22))

b) The optimum value of b) The optimum value of is very low and implies a hydrophilic binding site is very low and implies a hydrophilic binding site

c) c) RR-5 implies that resonance effects are important at position 5-5 implies that resonance effects are important at position 5

d) HB-INTRA equals 1 for H-bonding groups d) HB-INTRA equals 1 for H-bonding groups orthoortho to each other to each other (act. drops -086)(act. drops -086)

equals 0 if H-bonding groups are not equals 0 if H-bonding groups are not orthoortho to each other to each other

e) The steric parameter is no longer significant and is not presente) The steric parameter is no longer significant and is not present

LogLog 11CC

--0.034(0.034( ))22 -- 0.330.33 ++ 4.3(4.3(FF-- 5) 5) ++ 1.3 (1.3 (RR-- 5) 5) -- 1.7(1.7( ))22 ++ 0.73(3450.73(345-- HBD) HBD)

-- 0.86 (HB0.86 (HB-- INTRA) INTRA) -- 0.69(NHSO0.69(NHSO22) ) ++ 0.72(40.72(4-- OCO) OCO) -- 0.590.59


NH

O OH OH X

Y

Z

3

4

5

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Stage 6Stage 6 Optimum Structure and binding theory Optimum Structure and binding theory

11. Case Study11. Case Study

NH3

X

X

XXH

5

3

NH

NH

C

O

CH

OH

CH2OH

CH CH2OHC

O OH

RHN

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NOTES on the optimum structureNOTES on the optimum structure

• It has unusual NHCOCH(OH)CHIt has unusual NHCOCH(OH)CH22OH groups at positions 3 and OH groups at positions 3 and

55

• It is 1000 times more active than the lead compoundIt is 1000 times more active than the lead compound

• The substituents at positions 3 and 5The substituents at positions 3 and 5• are highly polar, are highly polar, • are capable of H-bonding, are capable of H-bonding, • are at the are at the metameta positions and are not positions and are not orthoortho to each other to each other• allow a favourable allow a favourable FF-5 parameter for the substituent at -5 parameter for the substituent at

position 5position 5

• The structure has a negligible (The structure has a negligible (22 value value

11. Case Study11. Case Study

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12. 3D-QSAR12. 3D-QSAR

• Physical properties are measured for the molecule as a wholePhysical properties are measured for the molecule as a whole• Properties are calculated using computer softwareProperties are calculated using computer software• No experimental constants or measurements are involvedNo experimental constants or measurements are involved• Properties are known as ‘Fields’Properties are known as ‘Fields’• Steric field - defines the size and shape of the moleculeSteric field - defines the size and shape of the molecule• Electrostatic field - defines electron rich/poor regions of Electrostatic field - defines electron rich/poor regions of

moleculemolecule• Hydrophobic properties are relatively unimportantHydrophobic properties are relatively unimportant

Advantages over QSARAdvantages over QSAR• No reliance on experimental valuesNo reliance on experimental values• Can be applied to molecules with unusual substituentsCan be applied to molecules with unusual substituents• Not restricted to molecules of the same structural classNot restricted to molecules of the same structural class• Predictive capability Predictive capability

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• Comparative molecular field analysis (CoMFA) - TriposComparative molecular field analysis (CoMFA) - Tripos• Build each molecule using modelling softwareBuild each molecule using modelling software• Identify the active conformation for each moleculeIdentify the active conformation for each molecule• Identify the pharmacophoreIdentify the pharmacophore

MethodMethod

NHCH3

OH

HO

HO

Active conformationActive conformation

Build 3DBuild 3Dmodelmodel

Define pharmacophoreDefine pharmacophore

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• Place the pharmacophore into a lattice of grid pointsPlace the pharmacophore into a lattice of grid points

MethodMethod

• Each grid point defines a point in spaceEach grid point defines a point in space

Grid pointsGrid points

..

.

.

.

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12. 3D-QSAR12. 3D-QSAR MethodMethod

• Each grid point defines a point in spaceEach grid point defines a point in space

Grid pointsGrid points

..

.

.

.

• Position molecule to match the pharmacophorePosition molecule to match the pharmacophore

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• A probe atom is placed at each grid point in turnA probe atom is placed at each grid point in turn

MethodMethod

• Probe atom = a proton or spProbe atom = a proton or sp33 hybridised carbocation hybridised carbocation

..

.

.

.Probe atomProbe atom

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• A probe atom is placed at each grid point in turnA probe atom is placed at each grid point in turn

MethodMethod

• Measure the steric or electrostatic interaction of the probe Measure the steric or electrostatic interaction of the probe atom with the molecule at each grid pointatom with the molecule at each grid point

..

.

.

.Probe atomProbe atom

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• The closer the probe atom to the molecule, the higher the steric The closer the probe atom to the molecule, the higher the steric energyenergy

• Can define the shape of the molecule by identifying grid points of Can define the shape of the molecule by identifying grid points of equal steric energy (contour line)equal steric energy (contour line)

• Favourable electrostatic interactions with the positively charged Favourable electrostatic interactions with the positively charged probe indicate molecular regions which are negative in natureprobe indicate molecular regions which are negative in nature

• Unfavourable electrostatic interactions with the positively charged Unfavourable electrostatic interactions with the positively charged probe indicate molecular regions which are positive in natureprobe indicate molecular regions which are positive in nature

• Can define electrostatic fields by identifying grid points of equal Can define electrostatic fields by identifying grid points of equal energy (contour line)energy (contour line)

• Repeat the procedure for each molecule in turnRepeat the procedure for each molecule in turn• Compare the fields of each molecule with their biological activityCompare the fields of each molecule with their biological activity• Can then identify steric and electrostatic fields which are favourable Can then identify steric and electrostatic fields which are favourable

or unfavourable for activityor unfavourable for activity

MethodMethod

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12. 3D-QSAR12. 3D-QSAR MethodMethod

Compound Biological Steric fields (S) Electrostatic fields (E)

activity at grid points (001-998) at grid points (001-098)

S001 S002 S003 S004 S005 etc E001 E002 E003 E004 E005 etc

1 5.1

2 6.8

3 5.3

4 6.4

5 6.1

Tabulate fields for each compound at each grid point

Partial least squares analysis (PLS)

QSAR equation Activity = aS001 + bS002 +……..mS998 + nE001 +…….+yE998 + z

. ..

..

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• Define fields using contour maps round a representative Define fields using contour maps round a representative moleculemolecule

MethodMethod

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13. 3D-QSAR -13. 3D-QSAR - CASE STUDYCASE STUDY

TacrineTacrine Anticholinesterase used in the treatment of Alzheimer’s diseaseAnticholinesterase used in the treatment of Alzheimer’s disease

N

NH2

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13. 3D-QSAR -13. 3D-QSAR - CASE STUDYCASE STUDY

ConclusionsConclusions• Large groups at position 7 are detrimentalLarge groups at position 7 are detrimental• Groups at positions 6 & 7 should be electron withdrawingGroups at positions 6 & 7 should be electron withdrawing• No hydrophobic effectNo hydrophobic effect

Conventional QSAR StudyConventional QSAR Study 12 analogues were synthesised to relate their activity with the 12 analogues were synthesised to relate their activity with the hydrophobic, steric and electronic properties of substituents at hydrophobic, steric and electronic properties of substituents at positions 6 and 7positions 6 and 7

N

NH2

R1

R2 6

7 9

CC LogLog 11 pICpIC5050 == -- 3.09 MR(R3.09 MR(R11) ) ++ 1.43F(R1.43F(R

11,,RR

22) ) ++ 7.007.00

Substituents: CHSubstituents: CH33, Cl, NO, Cl, NO22, OCH, OCH33, NH, NH22, F , F

(Spread of values with no correlation) (Spread of values with no correlation)

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13. 3D-QSAR - CASE STUDY13. 3D-QSAR - CASE STUDYCoMFA StudyCoMFA StudyAnalysis includes tetracyclic anticholinesterase inhibitors (II)Analysis includes tetracyclic anticholinesterase inhibitors (II)

N

NH2

R1

R2

R3

R4

R5II

1

2

3

8

7

• Not possible to include above structures in a conventional Not possible to include above structures in a conventional QSAR analysis since they are a different structural classQSAR analysis since they are a different structural class

• Molecules belonging to different structural classes must be Molecules belonging to different structural classes must be aligned properly according to a shared pharmacophorealigned properly according to a shared pharmacophore

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13. 3D-QSAR - CASE STUDY13. 3D-QSAR - CASE STUDYPossible AlignmentPossible Alignment

OverlayOverlay

Good overlay but assumes similar binding modesGood overlay but assumes similar binding modes

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13. 3D-QSAR - CASE STUDY13. 3D-QSAR - CASE STUDY

• A tacrine / enzyme complex was crystallised and analysedA tacrine / enzyme complex was crystallised and analysed• Results revealed the mode of binding for tacrineResults revealed the mode of binding for tacrine• Molecular modelling was used to modify tacrine to structure Molecular modelling was used to modify tacrine to structure

(II) whilst still bound to the binding site ((II) whilst still bound to the binding site (in silico)in silico)• The complex was minimised to find the most stable binding The complex was minimised to find the most stable binding

mode for structure IImode for structure II• The binding mode for (II) proved to be different from tacrineThe binding mode for (II) proved to be different from tacrine

X-Ray CrystallographyX-Ray Crystallography

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13. 3D-QSAR - CASE STUDY13. 3D-QSAR - CASE STUDY

• Analogues of each type of structure were aligned according to Analogues of each type of structure were aligned according to the parent structurethe parent structure

• Analysis shows the steric factor is solely responsible for Analysis shows the steric factor is solely responsible for activityactivity

7

6

• Blue areas - addition of steric bulk increases activityBlue areas - addition of steric bulk increases activity• Red areas - addition of steric bulk decreases activityRed areas - addition of steric bulk decreases activity

AlignmentAlignment

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13. 3D-QSAR -13. 3D-QSAR - CASE STUDYCASE STUDYPredictionPrediction6-Bromo analogue of tacrine predicted to be active (pIC6-Bromo analogue of tacrine predicted to be active (pIC5050 = 7.40) = 7.40)

Actual pICActual pIC5050 = 7.18 = 7.18

NBr

NH2

1 © patrick an introduction to medicinal chemistry 3/e chapter 13 quantitative structure- activity...

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