Quantitative Structure Activity Relationships QSAR and 3D-QSAR

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10/10/2011 1 Quantitative Structure Activity Relationships QSAR and 3D-QSAR Introduction Introduction Aims Aims To relate the biological activity of a series of compounds to their physicochemical To relate the biological activity of a series of compounds to their physicochemical parameters in a quantitative fashion using a mathematical formula parameters in a quantitative fashion using a mathematical formula Requirements Requirements Requirements Requirements Quantitative measurements for biological and physicochemical properties Quantitative measurements for biological and physicochemical properties Physicochemical Properties Physicochemical Properties Hydrophobicity Hydrophobicity of the molecule of the molecule Hydrophobicity Hydrophobicity of the molecule of the molecule Hydrophobicity Hydrophobicity of of substituents substituents Electronic properties of Electronic properties of substituents substituents Steric Steric properties of properties of substituents substituents Most common Most common properties studied properties studied

Transcript of Quantitative Structure Activity Relationships QSAR and 3D-QSAR

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Quantitative Structure Activity Relationships QSAR and 3D-QSAR

IntroductionIntroduction

••AimsAims••To relate the biological activity of a series of compounds to their physicochemical To relate the biological activity of a series of compounds to their physicochemical parameters in a quantitative fashion using a mathematical formulaparameters in a quantitative fashion using a mathematical formula••RequirementsRequirements••RequirementsRequirements••Quantitative measurements for biological and physicochemical propertiesQuantitative measurements for biological and physicochemical properties

••Physicochemical PropertiesPhysicochemical Properties

••HydrophobicityHydrophobicity of the moleculeof the moleculeHydrophobicityHydrophobicity of the moleculeof the molecule••HydrophobicityHydrophobicity of of substituentssubstituents••Electronic properties of Electronic properties of substituentssubstituents••StericSteric properties of properties of substituentssubstituents

Most commonMost commonproperties studiedproperties studied

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HydrophobicityHydrophobicity of the Moleculeof 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

••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 (straight line -- limited range of log limited range of log PP))

HydrophobicityHydrophobicity of the Moleculeof the Molecule

LogLog 11CC

0.75 log0.75 logPP ++ 2.302.30

Log (1/C)

. .... .

. ..

0 78 3 82

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

Log P0.78 3.82

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

HydrophobicityHydrophobicity of the Moleculeof the Molecule

LogLog 11CC

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

Log P oLog P

Log (1/C)

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

HydrophobicityHydrophobicity of of SubstituentsSubstituents-- the the substituentsubstituent hydrophobicityhydrophobicity constant (constant ())

NotesNotes::••A measure of a substituent’s hydrophobicity relative to hydrogenA measure of a substituent’s hydrophobicity relative to hydrogen••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 P values with log P of parent structurevalues with log P of parent structure

ExampleExample::Cl CONH2

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

ClCl = 0.71= 0.71 CONH CONH = = --1.491.4922

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Electronic Effects Electronic Effects Hammett Hammett SubstituentSubstituent Constant (Constant ())

NotesNotes::••The constant (The constant () is a measure of the e) is a measure of the e--withdrawing or ewithdrawing or e--donating influence of donating influence of substituentssubstituents••It can be measured experimentally and tabulatedIt can be measured experimentally and tabulated••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 dissociation constants of substituted benzoic acids with benzoic acid)substituted benzoic acids with benzoic acid)

+CO2H CO2 H

X X

X=HX=H KK HH == Dissociation constant Dissociation constant == [PhCO[PhCO 22--]][PhCO[PhCO 22H]H]

StericSteric FactorsFactorsTaft’s Steric Factor (Taft’s Steric Factor (EEss))

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

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 esterrepresents the rate of hydrolysis of the parent ester

••Limited to substituents which interact sterically with the tetrahedral transition state for Limited to substituents which interact sterically with the tetrahedral transition state for the reactionthe reaction••Cannot be used for substituents which interact with the transition state by resonance or Cannot be used for substituents which interact with the transition state by resonance or hydrogen bondinghydrogen bonding••May undervalue the steric effect of groups in an intermolecular process (i.e. a drug May undervalue the steric effect of groups in an intermolecular process (i.e. a drug b d )b d )binding to a receptor)binding to a receptor)

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StericSteric FactorsFactorsMolar Refractivity (Molar Refractivity (MRMR)) -- a measure of a substituent’s volumea 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

refraction)refraction)

StericSteric FactorsFactorsVerloop Steric ParameterVerloop Steric Parameter

-- calculated by software (STERIMOL)calculated by software (STERIMOL)-- gives dimensions of a substituentgives dimensions of a substituent-- can be used for any substituentcan be used for any substituent

B3

B4 B3

B2

B1

C

O

OH O C O

Example Example -- Carboxylic acidCarboxylic acid

L

B4

O

H

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bi d d ti

Environmental propertiesEnvironmental properties

The role of the molecular descriptors

biodegradation

bioconcentration

BOD

COD

half - life time

mobilityy

atmospheric persistance

.........................

.... and more.... and more

d ti it

The role of the molecular descriptors

conductivity

retention time

reological behaviours

.........................

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0D 0D -- countscounts0D 0D -- countscounts

Representations of a molecular structure

. .· ·

··· ·

··. .. .

C

C

C

C

C C

CC

C l C lH

H

H

H

1D 1D –– fragment countsfragment counts1D 1D –– fragment countsfragment counts

. .· · · ·. .

. .C

C

C

C

C C

CC

C l C lH

H

H

H

3D 3D -- geometricalgeometrical3D 3D -- geometricalgeometrical2D 2D -- topostructuraltopostructural2D 2D -- topostructuraltopostructural

· ···

· ·. ...

C C

C C

CC

CC

C l C lH

H

··· ·

··· ·

.

.

.

...

C C

C C

CC

CC

C l C lH

H

Cl Cl

ClCl

H

H

H

H

H

H

2D 2D -- topochemicaltopochemical2D 2D -- topochemicaltopochemical

molecular graphmolecular graph

Atom listAtom list 0D0D

countingcounting summingsumming

gridgrid--based QSAR based QSAR

Substructure listSubstructure list 1D1D

countingcounting

molecular geometrymolecular geometry

structural keysstructural keys

graph invariantsgraph invariants topographic topographic descriptorsdescriptors

2D2D techniquestechniques

interaction energy interaction energy valuesvalues

4D4D

x, y, z coordinatesx, y, z coordinates

geometrical geometrical descriptorsdescriptors

3D3D

topostructural topostructural descriptorsdescriptors

topochemical topochemical descriptorsdescriptors

topological information indicestopological information indices quantumquantum--chemical chemical descriptorsdescriptors

bulk descriptorsbulk descriptors

molecular surface molecular surface descriptorsdescriptors

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molecular graphmolecular graph graph invariantsgraph invariants

topostructural topostructural descriptorsdescriptors

topochemical topochemical descriptorsdescriptors

molecular geometrymolecular geometryx, y, z coordinatesx, y, z coordinates

topographic topographic descriptorsdescriptors

Wiener index, Hosoya Z indexZagreb indices, Mohar indicesRandic connectivity indexBalaban distance connectivity index

Wiener index, Hosoya Z indexZagreb indices, Mohar indicesRandic connectivity indexBalaban distance connectivity index

Kier-Hall valence connectivity indicesBurden eigenvaluesKier-Hall valence connectivity indicesBurden eigenvalues

3D-Wiener index3D-Balaban indexD/D index...............

3D-Wiener index3D-Balaban indexD/D index...............

topological information indicestopological information indices

Schultz molecular topological indexKier shape descriptorseigenvalues of the adjacency matrixeigenvalues of the distance matrixKirchhoff numberdetour indextopological charge indices...............

Schultz molecular topological indexKier shape descriptorseigenvalues of the adjacency matrixeigenvalues of the distance matrixKirchhoff numberdetour indextopological charge indices...............

total information content on .....mean information content on .....total information content on .....mean information content on .....

Burden eigenvaluesBCUT descriptorsKier alpha-modified shape descriptors2D autocorrelation descriptors...............

Burden eigenvaluesBCUT descriptorsKier alpha-modified shape descriptors2D autocorrelation descriptors...............

molecular geometrymolecular geometryx, y, z coordinatesx, y, z coordinates

geometrical geometrical descriptorsdescriptors

interaction energy interaction energy

valuesvalues

gridgrid--based QSAR based QSAR techniquestechniques

quantumquantum--chemical chemical

descriptorsdescriptors

volume volume

descriptorsdescriptors valuesvaluesdescriptorsdescriptors

CoMFA, GRIDG-WHIM descriptors............

CoMFA, GRIDG-WHIM descriptors............

van der Waals volumegeometric volume...........

van der Waals volumegeometric volume...........

chargeselectronegativitiessuperdelocalizability

chargeselectronegativitiessuperdelocalizability

molecular surfacemolecular surfacemolecular surfacemolecular surface

descriptorsdescriptors

gravitational indices3D-Morse descriptorsEVA descriptorsEEVA descriptorsWHIM descriptorsGETAWAY descriptors..............

gravitational indices3D-Morse descriptorsEVA descriptorsEEVA descriptorsWHIM descriptorsGETAWAY descriptors..............

hardnesssoftnessELUMO

EHOMO

..............

hardnesssoftnessELUMO

EHOMO

..............solvent-accessible surface areaCPSA descriptorsmolecular shape analysisMezey 3D shape analysis...........

solvent-accessible surface areaCPSA descriptorsmolecular shape analysisMezey 3D shape analysis...........

molecular surfacemolecular surfacemolecular surfacemolecular surface

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Based on these descriptors, 90 years later, Corwin Hansch proposed the first QSAR Based on these descriptors, 90 years later, Corwin Hansch proposed the first QSAR

approach.approach.

Some historical notes

Lipophilic, electronic and steric Lipophilic, electronic and steric

descriptors for orthodescriptors for ortho--, meta, meta--, and para, and para--

substituentssubstituents

19641964

Corwin HANSCHCorwin HANSCH

HanschHansch EquationEquation

••A QSAR equation relating various physicochemical properties to A QSAR equation relating various physicochemical properties to the biological activity of a series of compoundsthe 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 are Start with simple equations and elaborate as more structures are synthesisedsynthesised

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

LogLog 11CC

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

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HanschHansch EquationEquationExampleExample::Antimalarial activity of phenanthrene aminocarbinolsAntimalarial activity of phenanthrene aminocarbinols

(HO)HC

CH2NHR'R"

Conclusions:Conclusions:••Activity increases slightly as logActivity increases slightly as log PP (hydrophobicity) increases (note that the constant is only(hydrophobicity) increases (note that the constant is only

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

X

Y

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

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 must be orthogonal in Values must not be correlated for different properties (i.e. they must be orthogonal in value) value)

HanschHansch EquationEquationChoosing suitable substituentsChoosing suitable substituents

••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?

Substituent H Me Et nSubstituent H Me Et n--Pr nPr n--BuBu 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 1.960.10 0.56 1.03 1.55 1.96

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

Substituent H Me OMe NHCONHSubstituent H Me OMe NHCONH22 I CNI CN 0.00 0.56 0.00 0.56 --0.02 0.02 --1.30 1.12 1.30 1.12 --0.570.57MRMR 0.10 0.56 0.79 1.37 1.39 0.630.10 0.56 0.79 1.37 1.39 0.63

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Craig PlotCraig PlotCraig plot shows values for 2 different physicochemical properties for various substituentsCraig plot shows values for 2 different physicochemical properties for various substituents

ExampleExample::+

.75

1.0

. .CF3SO2

+ ++ -

.-.25

.75

.50

.25

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

.. . ........

CF3

Me

Cl Br I

OCF3

F

OCH

CH3CONH

CO2H

CH3CO

CN

NO2

CH3SO2

CONH2

SO2NH2

Ett-Butyl

SF5

- +

--1.0

-.75

-.50..

. NMe2

OCH3

OH

NH2

- +- -

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

••Choose a substituent from each quadrant to ensure orthogonalityChoose a substituent from each quadrant to ensure orthogonality

Craig PlotCraig Plot

••Choose a substituent from each quadrant to ensure orthogonalityChoose a substituent from each quadrant to ensure orthogonality

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

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ToplissTopliss SchemeSchemeUsed 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

H

4-Cl

4-CH34-OMe 3,4-Cl2

4-But 3-CF3-4-Cl

3-Cl 3-Cl 4-CF3 3-CF3-4-NO2

See CentralBranch

L E M

2,4-Cl2

4-NO2

3-NMe2 3-CH3

2-Cl

4-NO2

3-CF3

3,5-Cl2

3-NO2

4-F

4-NMe2

3-Me-4-NMe2

4-NH2

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

ActAct.. LittleLittlechangechange

Act.Act.

ToplissTopliss SchemeScheme

++ and/or +and/or +advantageousadvantageous

Favourable Favourable unfavourable unfavourable

++ and/or +and/or +disadvantageousdisadvantageous

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

(+(+ andand --))furtherfurther (+(+ and and --))

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

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ToplissTopliss SchemeSchemeAliphatic 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-BuPh ; CH2Ph CH2CH2Ph

ToplissTopliss SchemeSchemeExampleExample

M= More ActivityL= Less Activity

HighPotency

*

-MLEM

H4-Cl3,4-Cl24-Br4-NO2

12345

Biological Activity

ROrder ofSynthesis

R

SO2NH2

L Less ActivityE = Equal Activity

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ToplissTopliss SchemeSchemeExampleExample

Order ofSynthesis

R Biological Activity

HighPotency

NN

*

*

12345678

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

-LLMLMLM

*

M= More Activity

R N N

CH2CH2CO2H

yL= Less ActivityE = Equal Activity

BioBio--isosteresisosteres

Substituent C

O

CH3

CCH3

CNC CN

SCH3

O

S

O

CH3 S NHCH3

O

C

O

NMe2

••Choose Choose substituentssubstituents with similar physicochemical properties (with similar physicochemical properties (e.g. CN, NOe.g. CN, NO22 and and COMeCOMe could be biocould be bio--isosteresisosteres))

--0.550.55 0.400.40 --1.581.58 --1.631.63 --1.821.82 --1.511.51pp 0.500.50 0.840.84 0.490.49 0.720.72 0.570.57 0.360.36mm 0.380.38 0.660.66 0.520.52 0.600.60 0.460.46 0.350.35MRMR 11.211.2 21.521.5 13.713.7 13.513.5 16.916.9 19.219.2

3O O

COMeCOMe could be biocould be bio--isosteresisosteres))••Choose bioChoose bio--isosteresisosteres based on most important physicochemicalbased on most important physicochemical

property property (e.g. (e.g. COMeCOMe & & SOMeSOMe are similar in are similar in pp; ; SOMeSOMe and SOand SO22Me are similar in Me are similar in ))

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FreeFree--Wilson ApproachWilson Approach

••The biological activity of the parent structure is measured and compared with the The biological activity of the parent structure is measured and compared with the activity of analogues bearing different substituentsactivity of analogues bearing different substituents••An equation is derived relating biological activity to the presence or absence of An equation is derived relating biological activity to the presence or absence of

MethodMethod

q g g y pq g g y pparticular substituentsparticular 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 depending on whether the which is given the value 0 or 1 depending on whether the b ( )b ( )substituent (n) is present or notsubstituent (n) is present or not

••The contribution of each substituent (n) to activity is determined by the value of kThe contribution of each substituent (n) to activity is determined by the value of knn••Z is a constant representing the overall activity of the structures studiedZ is a constant representing the overall activity of the structures studied

FreeFree--Wilson ApproachWilson 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 features that cannot be Useful for quantifying the biological effects of molecular features that cannot be

AdvantagesAdvantages

quantified or tabulated by the Hansch method quantified or tabulated by the Hansch method

DisadvantagesDisadvantages

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

It i diffi lt t ti li h ifi b tit t d b d f ti itIt i diffi lt t ti li h ifi b tit t d b d f ti it••It is difficult to rationalise why specific substituents are good or bad for activityIt is difficult to rationalise why specific substituents are good 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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FreeFree--Wilson / Wilson / HanschHansch Approach Approach

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

AdvantagesAdvantages

Case StudyCase StudyQSAR analysis of pyranenamines (SK & F) QSAR analysis of pyranenamines (SK & F) (Anti(Anti--allergy compoundsallergy 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

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

CCLogLog 11

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

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

Conclusions:Conclusions:••Activity drops asActivity drops as increasesincreases••Activity drops as Activity drops as increasesincreases••Hydrophobic substituents are bad for activity Hydrophobic substituents are bad for activity -- unusualunusual••Any value of Any value of results in a drop in activityresults in a drop in activity••Substituents should not be eSubstituents should not be e--donating or edonating or e--withdrawing (activity falls if withdrawing (activity falls if is +ve or is +ve or --ve)ve)

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

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

AnomaliesAnomaliesa) 3a) 3--NHCOMe, 3NHCOMe, 3--NHCOEt, 3NHCOEt, 3--NHCOPr. 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 expectedand NHCOR at position 5 : Activity is greater than expected

c) NHSOc) NHSO R : Activity is worse than expectedR : Activity is worse than expectedc) NHSOc) NHSO22R : Activity is worse than expectedR : Activity is worse than expected

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

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

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

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5TheoriesTheories

b) OH, SH, NHb) OH, SH, NH22, and NHCOR at position 5, and NHCOR at position 5Possibly involved in HPossibly involved in H--bondingbonding

c) NHSOc) NHSO22R R Exception to HException to H--bonding theory bonding theory -- perhaps bad for steric or electronic reasonsperhaps bad for steric or electronic reasons

d) 3,5d) 3,5--(CF(CF33))22 and 3,5and 3,5--(NHMe)(NHMe)22The 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) 4e) 4--AcyloxyAcyloxyPresumably 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.

Stage 3Stage 3 Alter the QSAR equation to take account of new resultsAlter 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(NHSO 22))

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

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

(based on only 2 compounds though)(based on only 2 compounds though)(3,4,5(3,4,5--HBD) HBD) HBD at positions 3, 4,or 5 is good for activityHBD 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 positionsTerm = 2 if HBD groups are at two of these positionsTerm = 2 if HBD groups are at two of these positionsTerm = 0 if no HBD group is present at these positionsTerm = 0 if no HBD group is present at these positionsTerm = 0 if no HBD group is present at these positionsTerm = 0 if no HBD group is present at these positionsEach 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 is present (bad for activity by --0.63). 0.63). Equals zero if group is absent.Equals zero if group is absent.

((MM--VV) ) Volume of any Volume of any metameta substituent. Large substituents at substituent. Large substituents at metametaposition increase activityposition increase activity

44--OO--CO 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

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Stage 3Stage 3 Alter the QSAR equation to take account of new resultsAlter 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(NHSO 22))

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

++ 0.78(0.78(MM-- VV) ) ++ 0.72(40.72(4-- OCO) OCO) -- 0.750.75NoteNoteThe terms (3,4,5The terms (3,4,5--HBD), (NHSOHBD), (NHSO22), and 4), and 4--OO--CO are examples of indicator variables CO are examples of indicator variables used in the freeused in the free--Wilson approach and included in a Hansch equation Wilson approach and included in a Hansch equation

Stage 4Stage 437 Structures were synthesised to test steric and 37 Structures were synthesised to test steric and FF--5 parameters, as well as the effects of 5 parameters, as well as the effects of hydrophilic, Hhydrophilic, H--bonding groupsbonding groups

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

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

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

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Stage 5Stage 5 Revise EquationRevise Equation

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)

Case StudyCase StudyO O O

NH

O OH OH X

Y

Z

3

4

5

NOTESNOTESa) 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 (5). The equation is now parabolic (--0.034 (0.034 ())22))

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

CC

-- 0.86 (HB0.86 (HB -- INTRA) INTRA) -- 0.69(NHSO0.69(NHSO 22) ) ++ 0.72(40.72(4--OCO) OCO) -- 0.590.59

c) c) RR--5 implies that resonance effects are important at position 55 implies that resonance effects are important at position 5

d) HBd) HB--INTRA equals 1 for HINTRA equals 1 for H--bonding groups bonding groups orthoortho to each other to each other (act. drops (act. drops --086)086)equals 0 if Hequals 0 if H--bonding groups are not bonding groups are not orthoortho to each otherto 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

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

Case StudyCase Study

X

X

XXH

5

3

NH

NH

C

O

CH

OH

CH2OH

CH CH2OHC

RHN

NH3

XNH CH CH2OHC

O OH

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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 5OH groups at positions 3 and 5

Case StudyCase Study

••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 hydrogen bonding, are capable of hydrogen bonding, ••are at the are at the metameta positions and are not positions and are not orthoortho to each otherto each other••allow a favourable allow a favourable FF--5 parameter for the substituent at position 55 parameter for the substituent at position 5

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

3D3D--QSARQSAR

••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’

NotesNotes

••Properties are known as ‘Fields’Properties are known as ‘Fields’••Steric field Steric field -- defines the size and shape of the moleculedefines the size and shape of the molecule••Electrostatic field Electrostatic field -- defines electron rich/poor regions of moleculedefines electron rich/poor regions of molecule••Hydrophobic properties are relatively unimportantHydrophobic properties are relatively unimportant

Advantages over QSARAdvantages over QSAR

••No reliance on experimental valuesNo reliance on experimental values••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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3D3D--QSARQSAR

••Comparative molecular field analysis (CoMFA) Comparative molecular field analysis (CoMFA) -- TriposTripos••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

••Identify the pharmacophoreIdentify the pharmacophore

NHCH3

OH

HO NHCH3HO

HO

Active conformationActive conformation

Build 3DBuild 3Dmodelmodel

Define pharmacophoreDefine pharmacophore

3D3D--QSARQSAR

••Comparative molecular field analysis (CoMFA) Comparative molecular field analysis (CoMFA) -- TriposTripos••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

••Identify the pharmacophoreIdentify the pharmacophore

NHCH3

OH

HO NHCH3HO

HO

Active conformationActive conformation

Build 3DBuild 3Dmodelmodel

Define pharmacophoreDefine pharmacophore

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3D3D--QSARQSAR

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

MethodMethod

Grid pointsGrid points

..

.

.

.

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

3D3D--QSARQSARMethodMethod

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

Grid pointsGrid points

..

.

.

.

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

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3D3D--QSARQSAR

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

MethodMethod

..

.

.

.Probe atomProbe atom

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

3D3D--QSARQSAR

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

MethodMethod

..

.

.

.Probe atomProbe atom

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

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3D3D--QSARQSAR

••The closer the probe atom to the molecule, the higher the The closer the probe atom to the molecule, the higher the stericsteric energyenergy••Define the shape of the molecule by identifying grid points of equal Define the shape of the molecule by identifying grid points of equal stericsteric energy (contour energy (contour line)line)••FavorableFavorable electrostatic interactions with the positively charged probe indicate molecularelectrostatic interactions with the positively charged probe indicate molecular

MethodMethod

••FavorableFavorable electrostatic interactions with the positively charged probe indicate molecular electrostatic interactions with the positively charged probe indicate molecular regions which are negative in natureregions which are negative in nature••UnfavorableUnfavorable electrostatic interactions with the positively charged probe indicate electrostatic interactions with the positively charged probe indicate molecular regions which are positive in naturemolecular regions which are positive in nature••Define electrostatic fields by identifying grid points of equal energy (contour line)Define electrostatic fields by identifying grid points of equal 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••Identify Identify stericsteric and electrostatic fields which are and electrostatic fields which are favorablefavorable or or unfavorableunfavorable for activity for activity

3D3D--QSARQSARMethodMethod

. ..

..

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 etc1 5.12 6.83 5.3

Tabulate fields for each compound at each grid point

4 6.45 6.1

Partial least squaresanalysis (PLS)

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

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3D3D--QSARQSAR

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

MethodMethod