1. 1 © Patrick An Introduction to Medicinal Chemistry 3/e Chapter 13 QUANTITATIVE STRUCTURE- ACTIVITY RELATIONSHIPS (QSAR)

2. 1 © Contents 1.Introduction 2.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 & F 4.3.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-isosteres 10.Free-Wilson Approach (3 slides) 11.Case Study (10 slides) 12.3D-QSAR (10 slides) 13.3D-QSAR Case Study(7 slides) [62 slides]

3. 1 © 1. Introduction AimsAims To relate the biological activity of a series of compounds to their physicochemical parameters in a quantitative fashion using a mathematical formulaTo relate the biological activity of a series of compounds to their physicochemical parameters in a quantitative fashion using a mathematical formula RequirementsRequirements Quantitative measurements for biological and physicochemical propertiesQuantitative measurements for biological and physicochemical 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 common properties studied

4. 1 © 2. Hydrophobicity of the Molecule Partition Coefficient P = [Drug in octanol] in octanol] [Drug in water] High P High hydrophobicity

5. 1 © Activity of drugs is often related to PActivity of drugs is often related to P e.g. binding of drugs to serum albumin (straight line - limited range of log P) Binding increases as log P increasesBinding increases as log P increases Binding is greater for hydrophobic drugsBinding is greater for hydrophobic drugs Log1C      0.75 logP 0.75 logP+ 2.30 2.30 2. Hydrophobicity of the Molecule Log (1/C) Log P......... 0.78 3.82

6. 1 © Example 2 General anaesthetic activity of ethers (parabolic curve - larger range of log P values) Optimum value of log P for anaesthetic activity = log P o Log1C      - 0.22(logP) 2 + 1.04 logP 1.04 logP+ 2.16 2.16 2. Hydrophobicity of the Molecule Log P o Log (1/C)

7. 1 © QSAR equations are only applicable to compounds in the same structural class (e.g. ethers)QSAR equations are only applicable to compounds in the same structural class (e.g. ethers) However, log P o is similar for anaesthetics of different structural classes (ca. 2.3)However, log P o is similar for anaesthetics of different structural classes (ca. 2.3) Structures with log P ca. 2.3 enter the CNS easilyStructures with log P ca. 2.3 enter the CNS easily (e.g. potent barbiturates have a log P of approximately 2.0) Can alter log P value of drugs away from 2.0 to avoid CNS side effectsCan alter log P value of drugs away from 2.0 to avoid CNS side effects 2. Hydrophobicity of the Molecule

8. 1 © 3. Hydrophobicity of Substituents - the substituent hydrophobicity constant (p) 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 P’s with parent structureMeasured experimentally by comparison of log P’s with parent structure Example : Positive values imply substituents are more hydrophobic than HPositive values imply substituents are more hydrophobic than H Negative values imply substituents are lessNegative values imply substituents are less hydrophobic than H Benzene (LogP = 2.13) = 2.13) Chlorobenzene (LogP = 2.84) = 2.84) Benzamide (LogP = 0.64) = 0.64) ClCONH 2  Cl = 0.71  CONH = -1.49 2

9. 1 © The value of  is only valid for parent structuresThe value of  is only valid for parent structures It is possible to calculate log P using  valuesIt is possible to calculate log P using  values A QSAR equation may include both P and .A QSAR equation may include both P and . P measures the importance of a molecule’s overall hydrophobicity (relevant to absorption, binding etc)P measures the importance of a molecule’s overall hydrophobicity (relevant to absorption, binding etc)  identifies specific regions of the molecule which might interact with hydrophobic regions in the binding site  identifies specific regions of the molecule which might interact with hydrophobic regions in the binding site 3. Hydrophobicity of Substituents - the substituent hydrophobicity constant (p) Example : meta-Chlorobenzamide Cl CONH 2 Log P (theory) = log P (benzene) +  Cl +  CONH = 2.13 + 0.71 - 1.49 = 2.13 + 0.71 - 1.49 = 1.35 = 1.35 Log P (observed) = 1.51 2

10. 1 © 4. Electronic Effects 4.1 Hammett Substituent Constant (s) The constant (  ) a measure of the e-withdrawing or e- donating influence of substituentsThe constant (  ) a measure of the e-withdrawing or e- donating influence of substituents It can be measured experimentally and tabulatedIt can be measured experimentally and tabulated (e.g.  for aromatic substituents is measured by comparing the dissociation constants of substituted benzoic acids with benzoic acid) X=H K H = Dissociation constant Dissociation constant= [PhCO 2-] [PhCO 2 H]

11. 1 © X= electron withdrawing group (e.g. NO 2 )  X = log logKX K H = logK logK X - H Charge is stabilised by X Equilibrium shifts to right K X > K H Positive value 4.1 Hammett Substituent Constant (s)

12. 1 © X= electron donating group (e.g. CH 3 )  X = log logKX K H = logK logK X - H Charge destabilised Equilibrium shifts to left K X < K H Negative value 4.1 Hammett Substituent Constant (s)

13. 1 ©  value depends on inductive and resonance effects  value depends on whether the substituent is meta or para ortho values are invalid due to steric factors 4.1 Hammett Substituent Constant (s)

14. 1 © meta-Substitution EXAMPLES:  p (NO 2 )   m (NO 2 )  e-withdrawing (inductive effect only) e-withdrawing (inductive + resonance effects) 4.1 Hammett Substituent Constant (s) para-Substitution

15. 1 ©  m (OH)   p (OH)  e-withdrawing (inductive effect only) e-donating by resonance more important than inductive effect 4.1 Hammett Substituent Constant (s) EXAMPLES: meta-Substitution para-Substitution

16. 1 © QSAR Equation: Diethylphenylphosphates(Insecticides) log1C      2.282 2.282  - 0.348 0.348 Conclusion : e-withdrawing substituents increase activity 4.1 Hammett Substituent Constant (s)

17. 1 © 4.2 Electronic Factors R & F R - Quantifies a substituent’s resonance effectsR - Quantifies a substituent’s resonance effects F - Quantifies a substituent’s inductive effectsF - Quantifies a substituent’s inductive effects

18. 1 © 4.3 Aliphatic electronic substituents Defined by  IDefined by  I Purely inductive effectsPurely inductive effects Obtained experimentally by measuring the rates of hydrolyses of aliphatic estersObtained experimentally by measuring the rates of hydrolyses of aliphatic esters Hydrolysis rates measured under basic and acidic conditionsHydrolysis rates measured under basic and acidic conditions X= electron donating Rate  I = -ve X= electron withdrawing Rate  I = +ve Basic conditions: Rate affected by steric + electronic factors Gives  I after correction for steric effect Acidic conditions: Rate affected by steric factors only (see E s )

19. 1 © 5. Steric Factors Taft’s Steric Factor (E s ) Measured by comparing the rates of hydrolysis of substituted aliphatic esters against a standard ester under acidic conditionsMeasured by comparing the rates of hydrolysis of substituted aliphatic esters against a standard ester under acidic conditions E s = log k x - log k o k x represents the rate of hydrolysis of a substituted ester k o represents the rate of hydrolysis of the parent ester Limited to substituents which interact sterically with the tetrahedral transition state for the reactionLimited to substituents which interact sterically with the tetrahedral transition state for the reaction Cannot be used for substituents which interact with the transition state by resonance or hydrogen bondingCannot be used for substituents which interact with the transition state by resonance or hydrogen bonding May undervalue the steric effect of groups in an intermolecular process (i.e. a drug binding to a receptor)May undervalue the steric effect of groups in an intermolecular process (i.e. a drug binding to a receptor)

20. 1 © 5. Steric Factors Molar Refractivity (MR) - a measure of a substituent’s volume MR= (n2-1) (n 2 -2) x mol. wt. density Correction factor for polarisation (n=index of refraction) Defines volume

21. 1 © 5. Steric Factors Verloop Steric Parameter - calculated by software (STERIMOL) - gives dimensions of a substituent - can be used for any substituent - can be used for any substituent L B 3 B 4 B4B4 B3B3 B2B2 B1B1 Example - Carboxylic acid

22. 1 © 6. Hansch Equation A QSAR equation relating various physicochemical properties to the biological activity of a series of compoundsA QSAR equation relating various physicochemical properties to the biological activity of a series of compounds Usually includes log P, electronic and steric factorsUsually includes log P, electronic and steric factors Start with simple equations and elaborate as more structures are synthesisedStart with simple equations and elaborate as more structures are synthesised Typical equation for a wide range of log P is parabolicTypical equation for a wide range of log P is parabolic Log 1 C      - k (logP) 2 + k 2 logP logP+ k 3  + k 4 E s + k 5 1

23. 1 © 6. Hansch Equation Log1C      1.22 1.22  - 1.59 1.59  + 7.89 7.89 Conclusions: Activity increases if  is +ve (i.e. hydrophobic substituents)Activity increases if  is +ve (i.e. hydrophobic substituents) Activity increases if  is negative (i.e. e-donating substituents)Activity increases if  is negative (i.e. e-donating substituents) Example: Adrenergic blocking activity of  -halo-  -arylamines

24. 1 © Conclusions: Activity increases slightly as log P (hydrophobicity) increases (note that the constant is only 0.14)Activity increases slightly as log P (hydrophobicity) increases (note that the constant is only 0.14) Parabolic equation implies an optimum log P o value for activityParabolic equation implies an optimum log P o 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) Log1C      - 0.015 (logP) 2 + 0.14 logP 0.14 logP+ 0.27 0.27  X + 0.40 0.40  Y + 0.65 0.65  X + 0.88 0.88  Y + 2.34 2.34 6. Hansch Equation Example: Antimalarial activity of phenanthrene aminocarbinols

25. 1 © 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 value)values must not be correlated for different properties (i.e. they 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. Are any differences due to  or MR? No correlation in values Valid for analysing effects of  and MR. 6. Hansch Equation Substituent H Me Et n-Pr n-Bu  0.00 0.56 1.02 1.50 2.13 MR 0.10 0.56 1.03 1.55 1.96 Substituent H Me OMe NHCONH 2 I CN  0.00 0.56 -0.02 -1.30 1.12 -0.57 MR 0.10 0.56 0.79 1.37 1.39 0.63 Choosing suitable substituents

26. 1 © 7. Craig Plot Craig plot shows values for 2 different physicochemical properties for various substituents Example : -- ++ -  +  +  +  -  -  +  - 

27. 1 © Allows an easy identification of suitable substituents for a QSAR analysis which includes both relevant propertiesAllows an easy identification of suitable substituents for a QSAR analysis which includes both relevant properties 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 7. Craig Plot

28. 1 © 8. Topliss Scheme Used to decide which substituents to use if optimising compounds one by one (where synthesis is complex and slow) Example: Aromatic substituents

29. 1 © Rationale Replace H with para-Cl (+  and +  ) +  and/or +  advantageous favourable  unfavourable  +  and/or +  disadvantageous Act. Littlechange Act. add second Cl to increase  and  further replace with OMe (-  and -  ) replace with Me (+  and -  ) Further changes suggested based on arguments of  and steric strain 8. Topliss Scheme

30. 1 © Aliphatic substituents

31. 1 © 8. Topliss Scheme Example

32. 1 © Example

33. 1 © 9. Bio-isosteres Choose substituents with similar physicochemical properties ( e.g. CN, NO 2 and COMe could be bio-isosteres)Choose substituents with similar physicochemical properties ( e.g. CN, NO 2 and COMe could be bio-isosteres) Choose bio-isosteres based on most important physicochemical propertyChoose bio-isosteres based on most important physicochemical property (e.g. COMe & SOMe are similar in  p ; SOMe and SO 2 Me are similar in  )  -0.55 0.40-1.58-1.63-1.82-1.51  p 0.50 0.84 0.49 0.72 0.57 0.36  m 0.38 0.66 0.52 0.60 0.46 0.35 MR11.221.513.713.516.919.2

34. 1 © 10. Free-Wilson Approach The biological activity of the parent structure is measured and compared with the activity of analogues bearing different substituentsThe biological activity of the parent structure is measured and compared with the activity of analogues bearing different substituents An equation is derived relating biological activity to the presence or absence of particular substituentsAn equation is derived relating biological activity to the presence or absence of particular substituents Activity = k 1 X 1 + k 2 X 2 +.…k n X n + Z X n is an indicator variable which is given the value 0 or 1 depending on whether the substituent (n) is present or notX n is an indicator variable which is given the value 0 or 1 depending on whether the substituent (n) is present or not The contribution of each substituent (n) to activity is determined by the value of k nThe contribution of each substituent (n) to activity is determined by the value of k n Z is a constant representing the overall activity of the structures studiedZ is a constant representing the overall activity of the structures studied Method

35. 1 © 10. 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 features that cannot be quantified or tabulated by the Hansch methodUseful for quantifying the biological effects of molecular features that cannot be quantified or tabulated by the Hansch method Advantages Disadvantages A large number of analogues need to be synthesised to represent each different substituent and each different position of a substituentA large number of analogues need to be synthesised to represent each different substituent and each different position of a substituent 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)

36. 1 © 10. Free-Wilson / Hansch Approach It is possible to use indicator variables as part of a Hansch equation - see following Case StudyIt is possible to use indicator variables as part of a Hansch equation - see following Case Study Advantages

37. 1 © 11. Case Study QSAR analysis of pyranenamines (SK & F) (Anti-allergy compounds )

38. 1 © Stage 1 19 structures were synthesised to study  and  C Log1     -0.14  - 1.35( 1.35(  ) 2  0.72 0.72  and  = total values for  and  for all substituents Conclusions: Activity drops as  increasesActivity drops as  increases Hydrophobic substituents are bad for activity - unusualHydrophobic substituents are bad for activity - unusual Any value of  results in a drop in activityAny value of  results in a drop in activity Substituents should not be e-donating or e-withdrawing (activity falls if  is +ve or -ve)Substituents should not be e-donating or e-withdrawing (activity falls if  is +ve or -ve) 11. Case Study

39. 1 © Stage 2 61 structures were synthesised, concentrating on hydrophilic substituents to test the first equation Anomalies a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. Activity should drop as alkyl group becomes bigger and more hydrophobic, but the activity is similar for all three substituents b) OH, SH, NH 2 and NHCOR at position 5 : Activity is greater than expected c) NHSO 2 R : Activity is worse than expected d) 3,5-(CF 3 ) 2 and 3,5(NHMe) 2 : Activity is greater than expected e) 4-Acyloxy : Activity is 5 x greater than expected 11. Case Study

40. 1 © a) 3-NHCOMe, 3-NHCOEt, 3-NHCOPr. Possible steric factor at work. Increasing the size of R may be good for activity and balances out the detrimental effect of increasing hydrophobicity b) OH, SH, NH 2, and NHCOR at position 5 Possibly involved in H-bonding c) NHSO 2 R Exception to H-bonding theory - perhaps bad for steric or electronic reasons d) 3,5-(CF 3 ) 2 and 3,5-(NHMe) 2 The only disubstituted structures where a substituent at position 5 was electron withdrawing e) 4-Acyloxy Presumably acts as a prodrug allowing easier crossing of cell membranes. The group is hydrolysed once across the membrane. 11. Case Study Theories

41. 1 © Stage 3 Alter the QSAR equation to take account of new results Log1C      -0.30  - 1.35( 1.35(  ) 2 + 2.0(F 2.0(F-5)+ 0.39(345 0.39(345 -HBD)-0.63(NHSO 2 ) + 0.78(M - V)V)V)V)+ 0.72(4 0.72(4-OCO)- 0.75 0.75 Conclusions (F-5) e-withdrawing group at position 5 increases activity (based on only 2 compounds though) (3,4,5-HBD) H-bond donor group at positions 3, 4,or 5 is good for activity Term = 1 if a HBD group is at any of these positions Term = 1 if a HBD group is at any of these positions Term = 2 if HBD groups are at two of these positions Term = 2 if HBD groups are at two of these positions Term = 0 if no HBD group is present at these positions Term = 0 if no HBD group is present at these positions Each HBD group increases activity by 0.39 Each HBD group increases activity by 0.39 (NHSO 2 ) Equals 1 if NHSO 2 is present (bad for activity by -0.63). Equals zero if group is absent. (M-V) Volume of any meta substituent. Large substituents at meta position increase activity 4-O-CO Equals 1 if acyloxy group is present (activity increases by 0.72). Equals 0 if group absent 11. Case Study

42. 1 © Stage 3 Alter the QSAR equation to take account of new results Log1C      -0.30  - 1.35( 1.35(  ) 2 + 2.0(F 2.0(F-5)+ 0.39(345 0.39(345 -HBD)-0.63(NHSO 2 ) + 0.78(M - V)V)V)V)+ 0.72(4 0.72(4-OCO)- 0.75 0.75 The terms (3,4,5-HBD), (NHSO 2 ), and 4-O-CO are examples of indicator variables used in the free-Wilson approach and included in a Hansch equation 11. Case Study

43. 1 © Stage 4 37 Structures were synthesised to test steric and F-5 parameters, as well as the effects of hydrophilic, H-bonding groups Anomalies Two H-bonding groups are bad if they are ortho to each other Explanation Possibly groups at the ortho position bond with each other rather than with the receptor - an intramolecular interaction 11. Case Study

44. 1 © Stage 5 Revise Equation a) Increasing the hydrophilicity of substituents allows the identification of an optimum value for  (  = -5). The equation is now parabolic (-0.034 (  ) 2 ) optimum value for  (  = -5). The equation is now parabolic (-0.034 (  ) 2 ) b) The optimum value of  is very low and implies a hydrophilic binding site c) R-5 implies that resonance effects are important at position 5 d) HB-INTRA equals 1 for H-bonding groups ortho to each other (act. drops -086) equals 0 if H-bonding groups are not ortho to each other equals 0 if H-bonding groups are not ortho to each other e) The steric parameter is no longer significant and is not present Log1C      -0.034(  ) 2 -0.33  + 4.3(F 4.3(F-5)+ 1.3 (R 1.3 (R-5)- 1.7( 1.7(  ) 2 + 0.73(345 0.73(345-HBD) - 0.86 (HB 0.86 (HB-INTRA)- 0.69(NHSO 0.69(NHSO 2 )+ 0.72(4 0.72(4-OCO)- 0.59 0.59 11. Case Study

45. 1 © Stage 6 Optimum Structure and binding theory 11. Case Study NH 3 X X X XH

46. 1 © NOTES on the optimum structure It has unusual NHCOCH(OH)CH 2 OH groups at positions 3 and 5It has unusual NHCOCH(OH)CH 2 OH groups at positions 3 and 5 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 meta positions and are not ortho to each otherare at the meta positions and are not ortho to each other allow a favourable F-5 parameter for the substituent at position 5allow a favourable F-5 parameter for the substituent at position 5 The structure has a negligible (  2 valueThe structure has a negligible (  2 value 11. Case Study

47. 1 © 12. 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 ofElectrostatic field - defines electron rich/poor regions ofmolecule Hydrophobic properties are relatively unimportantHydrophobic properties are relatively unimportant Advantages 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 capabilityPredictive capability

48. 1 © 12. 3D-QSAR 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 Method Active conformation Build 3D model Define pharmacophore

49. 1 © 12. 3D-QSAR 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 Method Active conformation Build 3D model Define pharmacophore

50. 1 © 12. 3D-QSAR Place the pharmacophore into a lattice of grid pointsPlace the pharmacophore into a lattice of grid points Method Each grid point defines a point in spaceEach grid point defines a point in space Grid points.....

51. 1 © 12. 3D-QSAR Method Each grid point defines a point in spaceEach grid point defines a point in space Grid points..... Position molecule to match the pharmacophorePosition molecule to match the pharmacophore

52. 1 © 12. 3D-QSAR A probe atom is placed at each grid point in turnA probe atom is placed at each grid point in turn Method Probe atom = a proton or sp 3 hybridised carbocationProbe atom = a proton or sp 3 hybridised carbocation..... Probe atom

53. 1 © 12. 3D-QSAR A probe atom is placed at each grid point in turnA probe atom is placed at each grid point in turn Method Measure the steric or electrostatic interaction of the probeMeasure the steric or electrostatic interaction of the probe atom with the molecule at each grid point..... Probe atom

54. 1 © 12. 3D-QSAR The closer the probe atom to the molecule, the higher the steric energyThe closer the probe atom to the molecule, the higher the steric energy Can define the shape of the molecule by identifying grid points of equal steric energy (contour line)Can define the shape of the molecule by identifying grid points of equal steric energy (contour line) Favourable electrostatic interactions with the positively charged probe indicate molecular regions which are negative in natureFavourable electrostatic interactions with the positively charged probe indicate molecular regions which are negative in nature Unfavourable electrostatic interactions with the positively charged probe indicate molecular regions which are positive in natureUnfavourable electrostatic interactions with the positively charged probe indicate molecular regions which are positive in nature Can define electrostatic fields by identifying grid points of equal energy (contour line)Can 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 Can then identify steric and electrostatic fields which are favourable or unfavourable for activityCan then identify steric and electrostatic fields which are favourable or unfavourable for activity Method

55. 1 © 12. 3D-QSAR Method CompoundBiologicalSteric fields (S)Electrostatic fields (E) activity at grid points (001-998) at grid points (001-098) S001S002S003S004S005 etcE001E002E003E004E005 etc 15.1 26.8 35.3 46.4 56.1 Tabulate fields for each compound at each grid point Partial least squares analysis (PLS) QSAR equation Activity = aS001 + bS002 +……..mS998 + nE001 +…….+yE998 + z.....

56. 1 © 12. 3D-QSAR Define fields using contour maps round a representative moleculeDefine fields using contour maps round a representative molecule Method

57. 1 © 13. 3D-QSAR - CASE STUDY Tacrine Anticholinesterase used in the treatment of Alzheimer’s disease

58. 1 © 13. 3D-QSAR - CASE STUDY Conclusions 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 Study 12 analogues were synthesised to relate their activity with the hydrophobic, steric and electronic properties of substituents at positions 6 and 7 C  Log1   pIC pIC 50 = - 3.09 MR(R 1 )+ 1.43F(R 1.43F(R 1,R 2 )+ 7.00 7.00 Substituents: CH 3, Cl, NO 2, OCH 3, NH 2, F (Spread of values with no correlation)

59. 1 © 13. 3D-QSAR - CASE STUDY CoMFA Study Analysis includes tetracyclic anticholinesterase inhibitors (II) Not possible to include above structures in a conventional QSAR analysis since they are a different structural classNot possible to include above structures in a conventional QSAR analysis since they are a different structural class Molecules belonging to different structural classes must be aligned properly according to a shared pharmacophoreMolecules belonging to different structural classes must be aligned properly according to a shared pharmacophore

60. 1 © 13. 3D-QSAR - CASE STUDY Possible Alignment Overlay Good overlay but assumes similar binding modes

61. 1 © 13. 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 (II) whilst still bound to the binding site (in silico)Molecular modelling was used to modify tacrine to structure (II) whilst still bound to the binding site (in silico) The complex was minimised to find the most stable binding mode for structure IIThe complex was minimised to find the most stable binding mode 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 Crystallography

62. 1 © 13. 3D-QSAR - CASE STUDY Analogues of each type of structure were aligned according to the parent structureAnalogues of each type of structure were aligned according to the parent structure Analysis shows the steric factor is solely responsible for activityAnalysis shows the steric factor is solely responsible for activity 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 Alignment

63. 1 © 13. 3D-QSAR - CASE STUDY Prediction 6-Bromo analogue of tacrine predicted to be active (pIC 50 = 7.40) Actual pIC 50 = 7.18