Quantitative Structure-Activity Relationships : QSAR

Transcription

1 Quantitative Structure-Activity Relationships : QSAR

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3 ADME/Tox Absorption Distribution Metabolism Excretion Toxicity

4 ADME/Tox Absorption Distribution Metabolism Excretion Toxicity

5 Transporter Efflux system 4 Apical side (api) Microvilli ucleus Passive transcellular route 2. Passive paracellular route 3. Active carrier-mediated route 4. Efflux systems (P-glycoprotein etc.) 3 Tight Basolateral side (baso) Junction (PAMPA) Caco-2

6 Method of PAMPA 60% MeOH Solution of compounds hydrophobic filter 10% lecithin /1,9-decadiene buffer ph6.3 or 7.3 PAMPA: Parallel Artificial Membrane Permeation Assay

7 Descriptors for Classical QSAR Analyses log P oct : 1- / pk a ph : pk a ph 7.3 / SA HA, SA HD : van der Waals o (A 2 ) x 1/100

8 Total 60 compounds Test Compounds Peptide related compounds: 22 compounds Commercial drugs :38 compounds (shown as below) Compound log P oct Compound log P oct Compound log P oct norfloxacin coumarin 1.39 phenytoin 2.26 caffeine clonidine 1.43 diltiazem 2.80 hydrochlorothiazide hydrocortisone 1.61 alprenolol 2.89 theophylline prednisolone 1.62 propranolol 2.98 pirenzepine 0.10 acebutolol 1.71 labetalol 3.09 antipyrine 0.23 pindolol 1.75 ketoprofen 3.12 ranitidine 0.27 metoprolol 1.88 testosterone 3.32 acetaminophen 0.51 corticosterone 1.94 naproxen 3.34 nadolol 0.71 piroxicam 1.98 ibuprofen 3.50 practolol 0.79 dexamethasone 2.01 verapamil 3.79 trimethoprim 0.91 furosemide 2.03 imipramine 4.44 aminopyrine 1.00 oxprenolol 2.10 desipramine 4.54 chloramphenicol 1.14 salicylic acid 2.26 QSAR analysis 57 compounds

9 PAMPA Permeability of Structurally Diverse Compounds Compound desipramine imipramine testosterone Excluded from the QSAR equation log P oct log P app-pampa = 0.43 (± 0.09) log P oct 0.25 (± 0.08) pk a ph 1.07 (± 0.49) SA HA 1.00 (± 0.42) SA HD 4.98 (±0.31) n = 57 s = 0.33 r 2 = 0.76 q 2 = 0.74 Fujikawa, M. et al., Bioorg. Med. Chem., 13, 4721 (2005) (QSAR of PAMPA permeability)

10 Added Test Compounds Compound log P oct Compound log P oct Compound log P oct Chemicals Chemicals Agrochemicals 2,4-dichlorophenol chloroaniline 1.88 atrazine ,4-dimethylphenol cyanophenol 1.60 benthiocarb ,5-dichloronitorbenzene nitroaniline 1.39 biphenyl chloroaniline 1.90 aniline 0.90 BPMC chlorophenol 2.15 diethyl phtalate 2.47 diazinon methylphenol 1.95 dimethyl phtalate 1.56 DMTP nitoraniline 1.85 diphenylamine 3.50 IBP nitorphenol 1.79 hydroquinone 0.59 imidacloprid chloroaniline 1.88 phenol 1.47 MEP nitroaniline 1.37 pyrene 4.88 salithion nitrophenol 2.00 diphenylamine-2-carboxylic acid 4.36 tebufenozide 4.25 methoxyfenozide 3.70 halofenozide 3.22 chromafenozide 2.70 RH

11 Observed log P app-pampa -4.5 PAMPA Permeability Including Hydrophobic Compounds Previous compound set Added compounds set Calculated log P app-pampa Predicted log P app-pampa < -4.5: Increase with apparent hydrophobicity = Predicted log P app-pampa > -4.5: Decrease with apparent hydrophobicity Apparent hydrophobicity: log P app = log P oct α pk a ph

12 QSAR Equations for PAMPA Permeability Predicted log P app-pampa < -4.5 = log P app-pampa = 0.41 (± 0.09) log P oct 0.28 (± 0.07) pk a ph (±0.43) SA HA (± 0.40) SA HD (± 0.28) Predicted log P app-pampa > -4.5 n = 74 s = 0.35 r 2 = 0.77 log P app-pampa = (± 0.20) log P oct (± 0.15) pk a ph 3.69 (± 0.62) n = 23 s = 0.32 r 2 = 0.50 All compounds (Bilinear equation for log P app = log P oct 0.68 pk a ph log P app-pampa = 0.53 (± 0.10) log P app 1.18 (± 0.25) log(β10 logpapp + 1) 0.74 (± 0.35) SA HA 1.14 (± 0.40) SA HD 4.99 (± 0.24) n = 97 s = 0.36 r 2 = 0.72 q 2 = 0.68 log P app (opt) = 2.08 log β = -2.17

13 Structure of Agrochemicals CH 3 H C 2 H 5 OCOHCH 3 Cl O 2 imidacloprid BPMC CH 3 (H 3 C) 2 HC (H 3 C) 2 HC O O O P O S S P O OCH 3 IBP S C 2 H 5 O P C 2 H 5 O S H 3 CO P H 3 CO O S CH(CH 3 ) 2 O S diazinon salithion OCH 3 DMTP

14 Why Does PAMPA Permeability Decrease with Apparent Hydrophobicity for Hydrophobic Compounds? Donor Unstirred water layer Artificial membrane Unstirred water layer Retention? Barrier? Barrier? Acceptor

15 Membrane Retention Membrane Retention: [applied amount - (final amount in donor and acceptor compartments) ] x 100 R (%) = applied amount Compounds log P oct %R Compounds log P oct %R Compounds log P oct %R Drugs Chemicals Agrochemicals imipramine ,4-dichlorophenol atrazine testosterone ,4-dimethylphenol benthiocarb desipramine ,5-dichloronitorbenzene biphenyl methylphenol BPMC nitroaniline diazinon chloroaniline DMTP aniline IBP diethyl phtalate imidacloprid dimethyl phtalate MEP hydroquinone salithion phenol tebufenozide pyrene PAMPA permeability is also affected by membrane retention.

16 Main Absorption Mechanism Classified by P app-caco2 values in each direction api baso > baso api influx system Z= COOH, CH 2 COOH, CH 2 CH 2 COOH, CH 2 COH 2 Salicylic acid api baso api baso = baso api passive transcellular route Ac-Trp-H 2, Boc-Trp, CBZ-Trp, Fmoc-Trp, cyclo(trp-gly) Z= H, CH 2 OH api baso < baso api efflux system cyclo(trp-trp), Ac-Trp-Val-H 2, Ac-D-Trp-Val-H 2 Z H

17 Relationship between Caco-2 Cell and Unstirred PAMPA Permeability Coefficients log P app-caco2 P app-caco2 : api baso = baso api ( ) api baso > baso api ( ) api baso < baso api ( ) P app-caco2 (peptides related compounds, agrochemicals): Experimentally measured P app-caco2 (drug): Yazdanian, M. et al., Pharm. Res. (1998) log P app-pampa

18 Transporter Active transporters Z H Z= COOH, CH 2 COOH, CH 2 CH 2 COOH, CH 2 COH 2 O HO HO salicylic acid Efflux systems (P-gp?) H Ac-Trp-Val-H 2, Ac-D-Trp-Val-H 2 O H H O Cyclic (Trp-Trp) H 3 C O H CH CH 2 O H C H O H 2 H H

19 Transporters LAT PEPT1, PEPT2 MCT PT1 OAT, OATP OCT

20 P-glycoprotein (P-gp) ABC (ATP Binding Cassette) 12 Ca. 170 KDa) ATP 2 MDR (Multidrug Resistance-associated protein) (MDR1) BD: ucleotide Binding Domain ATP, 46(5), (2001), 2

21 Classical QSAR of P-gp Modulators Steroidal compounds log AR = log Mw Clog P H b n = 22 s = r = Flavonoids Wang, Lien, et al., J. Clin. Pharm. Ther. 28, 203 (2003) H b : total number of hydrogen bonds log 1/k d = Clog P H f lc n = 16 s = r = H f : heat of formation lc : number of atoms of the longest chain length Protein kinase C inhibitors log 1/IC 50 = 4.36 log Mw E lumo n = 11 s = r = 0.858

22 Free-Wilson Fujita-Ban Free-Wilson

23 Free-Wilson Substrates of Elastase Suc-X-Y-Ala-pA X,Y: amino acid Suc: succinyl pa: p-nitroanilide log (k cat /K m ) = Gly (X) Phe (X) Leu (X) Gly (Y) Leu (Y) Phe (Y) Pro (Y) le (Y) va (Y) Aba (Y) n = 89 s = 0.13 r 2 = 0.96 omizu et al., Int. J. Peptide Protein Res., 42, 216 (1993)

24 (Principal Component Analysis: PCA) SIMCA (Soft Independent Modeling of Chemical Analogy)

25 3D-QSAR Comparative Molecular Field Analysis (CoMFA) Voronoi Field analysis (VFA) 3D-Similarity CATALYST VolSurf

26 3D-QSAR Comparative Molecular Field Analysis (CoMFA) Voronoi Field analysis (VFA) 3D-Similarity CATALYST VolSurf

27 X H Cl H 3D-Lattice Y CoMFA (1) (2) (MM/MO (3) (4) (5) Partial Least Squares: PLS [C(sp 3 ), +1] Probe Activity = a + [CoMFA steric and/or electrostatic terms] + b log P + c (log P) (6)

28 CoMFA Fields Red: Electro-negatively favorable region Blue: Electro-positively favorable region Green: Sterically favorable region Orange: Sterically unfavorable region

29 17. Fujikawa, M. et al., Bioorg. Med. Chem., 13, 4721 (2005) (QSAR of PAMPA permeability) 18. omizu, M. et al., Int. J. Peptide Protein Res., 42, 216 (1993) (QSAR of elastase substrates) 19. Cramer, R. D., III et al., J. Am. Chem. Soc., 110, 5959 (1988) (CoMFA)