S
1
Supporting Information A Comparison of Methods for Modeling Quantitative Structure-Activity Relationships Jeffrey J. Sutherland, Lee A. O’Brien and Donald F. Weaver.
Contents A.1. Datasets and literature references ........................................................................................... 2 ACE............................................................................................................................................. 2 AchE ........................................................................................................................................... 3 BZR............................................................................................................................................. 7 COX2 ........................................................................................................................................ 13 DHFR........................................................................................................................................ 22 GPB, THER, THR .................................................................................................................... 34 A.2. Values of q2L20%O and q2L33%O, and thresholds for defining outliers..................................... 35 A.3. Alignment procedures for CoMFA, CoMSIA ...................................................................... 40 A.4. Description of grids used for CoMFA, CoMSIA.................................................................. 42 A.5. 2.5D descriptors used as inputs for neural network models ................................................. 43 A.6. Notes on electronic files........................................................................................................ 43
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A.1. Datasets and literature references ACE The following compounds are drawn incorrectly in the original publication;1 they are corrected in the electronic files: mol_35, mol_53, mol_54, mol_55, mol_56, thiol_2, thiol_4, thiol_27, thiol_28. Table A.1.1. ACE inhibitor sets Training set MOL_07, MOL_08, MOL_09, MOL_12, MOL_14, MOL_15, MOL_16, MOL_18, MOL_19, MOL_20, MOL_21, MOL_22, MOL_24, MOL_25, MOL_26, MOL_29, MOL_30, MOL_31, MOL_33, MOL_34, MOL_37, MOL_38, MOL_41, MOL_42, MOL_43, MOL_45, MOL_46, MOL_47, MOL_49, MOL_50, MOL_51, MOL_52, MOL_53, MOL_56, MOL_57, MOL_59, MOL_63, MOL_65, MOL_66, MOL_68, COO_23A, COO_23J, COO_24C, COO_25A, COO_25E, COO_26A, COO_26C, COO_26H, SQ29852, SQ29852_2B, SQ29852_2Q, SQ29852_2R, SQ29852_2T, SQ29852_2U, SQ29852_2V, SQ29852_2W, SQ29852_2Y, SQ29852_2Z, SQ29852_2X, SQ29852_2E, SQ29852_2K, SQ29852_2I, THIOL_2, THIOL_4, THIOL_5, THIOL_7A, THIOL_7B, THIOL_9, THIOL_10, THIOL_14, THIOL_18, THIOL_20A, THIOL_20B, THIOL_27, THIOL_30A, THIOL_30B Test set MOL_01, MOL_02, MOL_03, MOL_04, MOL_05, MOL_06, MOL_10, MOL_11, MOL_13, MOL_17, MOL_23, MOL_27, MOL_28, MOL_32, MOL_35, MOL_36, MOL_39, MOL_40, MOL_44, MOL_48, MOL_54, MOL_55, MOL_58, MOL_60, MOL_61, MOL_62, MOL_64, MOL_67, COO_23E, COO_24A, SQ29852_2A, SQ29852_2P, SQ29852_2S, SQ29852_2G, SQ29852_2H, THIOL_12, THIOL_22, THIOL_28 ACE references (1) Depriest, S. A.; Mayer, D.; Naylor, C. B.; Marshall, G. R. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors - a comparison of CoMFA models based on deduced and experimentally determined active-site geometries. J. Am. Chem. Soc. 1993, 115, 5372-5384.
2
S AchE Table A.1.2. Structures (families) of AchE inhibitors A.2
A.1 N R1
N
R3
R1
N R2
B.2
B.1
N R2
O
3 4
N
1 N
R1
O
3
2
R2
2
4 R1
O
N
N
1 R1 3
4
D.3
O N
1
R2
1 2
R1
3
4
O
R2
2
R1
R2
2
R1
R2
O
D.1
D.2
N
1 N
O
C
R3
N
3
4
Table A.1.3. AchE inhibitors a
Name 1-1 1-2 1-3a 1-3b 1-3c 1-3d 1-3e 1-3f 1-3g 1-3h 1-3i 1-3j 1-3k 1-3l 1-3m 1-3n 1-3o
R1 PhCOPhCOPhCOp-OCH3PhCOp-FPhCOp-NO2PhCOp-pyridineCOcyclohexylCOCH3COCH3CH2COCH3COCH3COCH3COCH3COCH3CH2CH3COCH3CO-
R2 HMePhPhPhPhPhPhPhPhm-OCH3Php-OCH3Phm-FPhp-FPhPhp-pyridineMe-
R3 H H H H H H H H H H H H H H H H H
Family A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1
IC50 (nM) 560 170 35 590 18 5.4 64 9400 52 830 46 700 65 205 12000 108 660
Set b
1 1 1 1 1 1 2 1 1 1 1 2 2 1 1 1 2
3
S 2-3b 2-3c 2-3d 2-3e 2-3f 2-3g 2-3h 2-3i 2-3j 2-3k 2-3l 2-3m 2-3n 2-3o 2-3p 2-3r 2-12 2-14 2-15 2-21 2-22 2-23 2-25 2-26 2-27 2-28 2-29 2-30 2-24 2-31 2-32 2-33 2-34 2-35 2-36 1-10 1-13 1-14 1-15 1-17 1-18 1-19 1-20 1-21 1-22 1-23 1-24 1-25 1-16
o-MePhCOm-MePhCOp-MePhCOo-NO2PhCOm-NO2PhCOp-NO2PhCOp-OMePhCOp-CHOPhCOp-ClPhCOp-FPhCOp-MeCOPhCOp-(PhCH2SO2)PhCOo-pyridineCOm-pyridineCOp-pyridineCOcyclohexylCOPhCH2PhCOPhCOp-(PhCH2SO2)PhCOp-(PhCH2SO2)PhCOp-(PhCH2SO2)PhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOPhCOH 4-NO2 4-NO2 4-NO2 4-NH2 4-NHCOMe 4-NHCOPh 4-OMe 4-CONHCH2Ph 4-COPh 6-NO2 6-NH2 6-NHCOPh 4-NO2
HHHHHHHHHHHHHHHHHEtPhCH2MeEtPhMeMeMeMeMe MeMeMeMeMeMeMeMeH H 4-OMe 4-Cl H H H H H H H H H Me-
H H H H H H H H H H H H H H H H H H H H H H 2-Me 3-Me 4-Me 2-NO2 3-NO2 4-NO2 H PhCH2CH2PhCH=CHCH2-
PhCOcyclopropyl-CH2cyclohexyl-CH2-
adamantylCH2-
A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.2 A.2 A.2 A.2 A.2 A.2 A.2 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.2
1000 470 180 880 230 55 88 120 180 85 51 29 800 69 39 1600 46000 130 940 0.6 0.3 0.6 770 145 41000 14000 370 3300 26000 13000 54000 52000 38000 410 24000 30 12.5 440 240 8.8 2.8 1.2 8 2.2 2.4 9 11 340 6800
2 1 1 2 1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 2 2 1 1 1 2 1 1 1 1 2 1 1 1 2 2 2 1 2 1
C
98
1
O
1-9
N
4
S O
O2N
1-11
C
27000
2
C
3000
1
C
13
2
C
1100
1
C
13
2
C
1000
1
C
17
1
C
1600
2
C
23
2
N
C
1200
2
N
C
800
1
C
4.2
1
C
13
2
C
4.5
2
C
270
2
N O O
O2N
1-12
N O
O
1-26
N N O
O
1-29
N
O
3-12a
MeO MeO O
1-31a
N
N
1-31b
O N
1-31c O
1-31d
N O
O
1-34 N O
1-35 N H O
N
1-37 N H
O N
1-38
N H
O O N
1-39 N H
Cl
1-40
N O
O
5
S 2-9
PhCO(CH2)3-
C
530
2
C
150
1
C
3300
1
C
30
1
C
2100
1
C
15000
1
C
300
2
C
4400
2
O
3-9 O
3-13n
MeO MeO O
3-13o
MeO MeO
O
3-13c O
3-13d OH
3-17
MeO MeO MeO
3-18 MeO
3-13e 5,6-diOMe H D.1 5.7 1 3-13f 6-OMe H D.1 81 2 3-13g 5-OMe H D.1 6.4 1 3-13h 4-OMe H D.1 12 1 3-13i 6.7-diOMe H D.1 85 1 3-13j 5,7-diOMe H D.1 25 1 3-13k 4,7-diOMe H D.1 36 1 3-13l 4,5-diOMe H D.1 20 1 3-13m 5,6,7-triOMe H D.1 13 2 3-16a 5,6-diOMe 2-Me D.1 10 1 3-16b 5,6-diOMe 3-Me D.1 2 1 3-16c 5,6-diOMe 4-Me D.1 40 1 3-16d 5,6-diOMe 2-NO2 D.1 160 1 3-16e 5,6-diOMe 3-NO2 D.1 4 2 3-16f 5,6-diOMe 4-NO2 D.1 100 1 3-13a 5,6-diOMe PhCOD.2 >10000 2 3-13b 5,6-diOMe HD.2 5400 2 3-16g 5,6-diOMe cyclohexylCH2D.2 8.9 1 3-16h 5,6-diOMe PhCH2CH2D.2 180 2 3-15a 5,6-diOMe C D.3 480 1 3-15b 5,6-diOMe N D.3 94 2 a names are formed by hyphenating the reference number and the label given to the compound in the reference; e.g. 1-2 is compound 2 in reference 1. b training set and test set compounds are indicated as 1 and 2.
6
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7
AchE references (1) Sugimoto, H.; Tsuchiya, Y.; Sugumi, H.; Higurashi, K.; Karibe, N. et al. Synthesis and structure-activity relationships of acetylcholinesterase inhibitors: 1-benzyl-4-(2-phthalimidoethyl)piperidine and related derivatives. J. Med. Chem. 1992, 35, 4542-4548. (2) Sugimoto, H.; Tsuchiya, Y.; Sugumi, H.; Higurashi, K.; Karibe, N. et al. Novel piperidine derivatives. Synthesis and anti-acetylcholinesterase activity of 1-benzyl-4-[2-(N-benzoylamino)ethyl]piperidine derivatives. J. Med. Chem. 1990, 33, 1880-1887. (3) Sugimoto, H.; Iimura, Y.; Yamanishi, Y.; Yamatsu, K. Synthesis and structure-activity relationships of acetylcholinesterase inhibitors: 1-benzyl-4-[(5,6-dimethoxy-1-oxoindan-2- Yl)methyl]piperidine hydrochloride and related compounds. J. Med. Chem. 1995, 38, 4821-4829.
BZR Table A.1.4. Structures (families) of BZR ligands A.1 9
R4
O
R2
R4
N
R3 R1
O
NHCH3
N
R3
A.12
R1
R2
O-
N
R4 R3
A.13 O
A.14
R1
A.15 R1
N
N
N
N
R4
N O
N
N
R2
R3
N
R3
N
R4
A.8
N+
R4
O-
R3
O
H N
N+
N
R4
R3
A.7
N R4
N
R3
A.6
O
H N N
S
N
R3
A.5
O
H N R4
N
6
A.4
O
H N
S
N
8 7
A.3
A.2
R1
S R4
N R2
R4
N
R1 N
8
N
R3
R3
N
7 R4
R5
S
A.17
O
H N
A.18
A.19
R1
A.20
N
N
N
R1
N
N
N
N
N R4
8
R4
R4
R4
R3
R3
R3
R3
A.21
A.22
N
N
N
N
R4
A.23
R1
A.24
H N
COR1
R4
N
N N
9
N
8
R3 N
R4
O
N
R4
H
R3
R3
A.25
A.26
N COR1
R4 10 9 8 7
H N
N
7
O
O
O
COOC2H5 N
N
8
N
N
COR1
R4
N
A.27
N
Table A.1.5. BZR ligands a
Name
Ro05-3061 Ro05-4865 Ro05-6820 Ro05-6822 Nordazepam Diazepam Ro07-3953 Ro07-4065 Delorazepam Ro05-2904 Ro14-3074 Nitrazepam Ro05-4435 Flunitrazepam Clonazepam
R1 -H -Me -H -Me -H -Me -H -Me -H -H -H -H -H -Me -H
R2 -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H
R3 -Ph -Ph -C6H4-2-F -C6H4-2-F -Ph -Ph -C6H3-2,6-F -C6H3-2,6-F -C6H4-2-Cl -Ph -C6H4-2-F -Ph -C6H4-2-F -C6H4-2-F -C6H4-2-Cl
R4 -7-F -7-F -7-F -7-F -7-Cl -7-Cl -7-Cl -7-Cl -7-Cl -7-CF3 -7-N3 -7-NO2 -7-NO2 -7-NO2 -7-NO2
R5
Family A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1
IC50 (µ µM)
Set
0.04 0.017 0.0074 0.0051 0.0094 0.0081 0.0016 0.0041 0.0018 0.013 0.0053 0.01 0.0015 0.0038 0.0018
1 1 1 1 1 1 1 1 1 1 2 2 1 1 1
b
S Ro05-3590 Ro20-7736 Ro05-3072 Ro05-4318 Ro20-1815 Ro05-4619 Ro05-3308
-H -Me -H -Me -Me -H -H
-H -H -H -H -H -H -H
-C6H4-2-CF3 -C6H4-2-F -Ph -Ph -C6H4-2-F -C6H4-2-Cl -Ph
Ro12-6377
-Me
-H
-C6H4-2-F
Ro05-9090 Ro05-4528 Ro20-2541 Ro20-2533 Ro20-5747 Ro20-5397 Ro20-3053 Ro05-3343 Ro05-2921 Ro05-4336 Ro07-4419 Ro05-4520 Ro05-3546 Ro13-0699 Ro07-6198 Ro20-8895 Ro13-0593 Ro13-0882 Ro22-6762 Ro20-8065 Ro20-8552 Ro05-2750 Ro14-2312 Ro17-2221 Halazepam Pinazepam
-Me -Me -Me -H -H -H -H -H -H -H -H -Me -H -Me -H -H -Me -Me -Me -H -H -H -Me
-H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H
-Ph -Ph -C6H4-2-F -Ph -Ph -Ph -C6H4-2-F -Ph -Ph -C6H4-2-F -C6H3-2,6-F -C6H4-2-F -Ph -C6H4-2-F -C6H3-2,6-F -C6H4-2-F -C6H4-2-F -C6H4-2-F -Ph -C6H4-2-F -C6H4-2-F -Ph -C6H4-2-F -Ph -Ph -Ph
-H
Prazepam Ro06-9098 Ro20-1310 Ro05-7094 Ro07-1986 Ro07-2750
-CH2CH2NH2
-CH2CF3 -CH2C≡CH -CH2cycloPr -CH2OCH3 -t-Bu -CH(CH3) CONHCH3 -CH2CH2NH2 -CH2CH2OH
-7-NO2 -7-NHOH -7-NH2 -7-NH2 -7-NH2 -7-NH2 -7-NHCOCH3 -7NHCONHCH3 -7-CH2NH2 -7-CN -7-CN -7-Et -7-CH=CH2 -7-CHO -7-COCH3
9
A.1 A.1 A.1 A.1 A.1 A.1 A.1
0.0035 0.096 0.386 0.46 0.065 0.075 >1
1 1 1 1 1 1 3
A.1
0.455
2
-7-Cl -7-Cl
A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1
>1 0.38 0.03 0.036 0.024 0.043 0.018 >1 0.35 0.021 0.019 0.014 0.32 0.15 0.028 0.019 0.072 0.3 0.04 0.0036 0.014 0.037 >1 0.26 0.092 0.0925
3 1 2 1 1 1 2 3 1 1 1 1 1 1 1 1 1 2 1 1 1 2 3 1 1 1
-Ph
-7-Cl
A.1
0.11
2
-H -H
-Ph -Ph
-7-NO2 -7-Cl
A.1 A.1
0.43 0.62
2 2
-H
-Ph
-7-Cl
A.1
>1
3
-H -H
-C6H4-2-F -C6H4-2-F
-7-Cl -7-Cl
A.1 A.1
0.0083 0.0245
1 1
-7-SO2N(CH3)2
-6-Cl -6-Cl -8-Cl -8-CH3 -9-Cl -6,8-Cl -6,7-Cl -6,7-Cl -6-Me,7-Cl -6,8-Cl -6-NH2,8-Cl
-CH2CH (OH)CH2OH -t-Bu -CH2CO2H -H
-H
-C6H4-2-F
-7-Cl
A.1
0.14
2
-H -H -H
-C6H4-2-Cl -C6H4-2-F -Me
-7-NO2 -7-Cl
A.1 A.1 A.1
0.3 >1 >1
2 3 3
-H
-H
-7-Cl
A.1
0.034
1
Tetrazepam
-Me
-H
-7-Cl
A.1
0.034
2
Ro05-3328
-H
-H
-7-Cl
A.1
0.087
2
Ro10-3580 Ro22-4683 Ro07-5096 Ro05-3663 Desmethyltetrazepam
-1cyclohexene -1cyclohexene
cyclohexane
S 10 Bromazepam Ro11-4878 Meclonazepam Ro11-6896 Ro07-4532 Ro06-7263 Oxazepam Temazepam Lorazepam Ro20-7078 Clorazepate Ro11-8125 Ro08-6739 Ro08-9212 Ro10-2643 Premazepam Ro05-3395 Ro05-2181 Ro05-2881 Ro05-3636 Ro15-8852 Chlordiazepoxide Demoxepam Medazepam Clobazam Desmethylclobazam U-35005 Estazolam Alprazolam Triazolam alpha-hydroxytriazolam Adinazolam Ro11-5073 Ro11-6679 Ro17-4582 Etizolam Ro11-1465 Ro11-7800 Midazolam alpha-hydroxymidazolam Ro15-8670 Ro16-0529 Ro21-5205
-H -H -H -Me -Me -Cl -H -Me -H -Me -H
-H -α-Me -α-Me -α-Me -(CH3)2 -Me -OH -OH -OH -Cl -CO2H
-H -H -Me -Me -H
-H -H -H -Me -Me
Ro22-1892
-H
Ro22-0992 Ro21-8137 Ro21-8482 Ro14-1359
-H -H
-2-pyridyl -C6H4-2-F -C6H4-2-Cl -C6H4-2-F -Ph -Ph -Ph -Ph -C6H4-2-Cl -C6H4-2-F -Ph -C6H4-2-Cl -Ph -C6H4-2-Cl -C6H4-2-Cl -Ph -Ph -Ph -Ph -C6H4-2-F -C6H4-2-Cl
-7-Br -7-Cl -7-NO2 -7-NO2 -7-Cl -7-Cl -7-Cl -7-Cl -7-Cl -7-Cl -7-Cl -H -Cl -Cl -Cl -H -Cl -Cl -Cl -NO2
A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.2 A.2 A.2 A.3 A.4 A.5 A.5 A.5 A.5 A.5
0.018 0.0035 0.0012 0.007 >1 0.049 0.018 0.016 0.0035 0.0053 0.059 0.037 0.07 0.0039 0.0094 0.17 >1 >5 >1 >1 0.726
2 1 1 2 3 1 1 1 2 1 2 1 1 2 2 2 3 3 3 3 2
-Ph
-Cl
A.6
0.352
2
-Me
-Ph -Ph -Ph
-Cl -Cl -Cl
A.7 A.8 A.12
0.31 0.87 0.13
2 2 2
-H
-Ph
-Cl
A.12
0.21
1
-Me -H -Me -Me
-H -H -H -H
-C6H4-2-Cl -Ph -Ph -C6H4-2-Cl
-H -Cl -Cl -Cl
A.13 A.13 A.13 A.13
0.0043 0.0085 0.02 0.004
1 1 1 1
-CH2OH
-H
-Ph
-Cl
A.13
0.0042
2
-CH2N(CH3)2
-H -α-Me -α-Me
-H
-Ph -C6H4-2-F -C6H4-2-F -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-F
-Cl -Cl -NO2 -H -Et -Cl -Cl -8-Cl
A.13 A.13 A.13 A.14 A.14 A.14 A.14 A.15
0.135 0.0033 0.004 0.0035 0.0031 0.0014 0.0029 0.0048
1 2 1 1 1 2 1 1
-CH2OH
-H
-C6H4-2-F
-8-Cl
A.15
0.0045
2
-H -H -H
-CO2Et -CO2C(CH3)3 -CO2CH3
-Ph -Ph -C6H4-2-F
-8-Cl -7-Cl -8-Cl
A.15 A.15 A.15
0.015 0.014 0.0074
1 2 1
-C6H4-2-F
-8-Cl
A.15
0.012
2
-C6H4-2-Cl -C6H4-2-F -C6H4-2-Cl -C6H4-2-F
-8-Cl -8-Cl -8-Cl -Cl
A.15 A.15 A.15 A.17
0.013 0.0035 0.026 0.07
1 1 2 2
-Me -Me -Me -Me -Me -CH2NH2 -Me
-CH2N(CH3)2
-
CO2CH(CH3)2 -CO2H -CONH2 -CONH2
O
S 11 Ro15-8867 Ro14-7187 Ro13-9868 Ro14-5921 Ro14-0304 Ro14-2652 Ro15-9270 Ro14-0609 Ro15-2201 Ro15-0791 Ro15-2200 Ro15-3929 Ro14-3930 Ro14-5568 Ro22-1274 Ro22-1251 Ro22-1366 Ro22-2038 Ro22-3245 Ro22-3148 Ro22-3147 Ro22-0780 Ro22-2466 Ro14-7181 Ro16-4234 Ro14-5974 Ro15-4941 Ro14-5975 Ro16-3607 Ro16-6624 Ro16-3774 Ro16-0071 Ro16-5824 Ro16-8912 Ro16-4261 Ro16-6127 Ro16-6048 Ro16-6950 Ro16-4019 Ro16-3031
-Me -Me -H -Me -CH2NH2 -Me -CO2CH3 -CO2Et -CO2Et -CO2Et -CONH2 -H -Me -Me -NH2 -H
-NH2 -NH2 -OEt -OEt -OEt -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-t-Bu -O-n-Pr -O-i-Pr
-C6H4-2-Cl -Ph -Ph -C6H4-2-F -C6H4-2-F -C6H4-2-F -C6H4-2-Cl -C6H4-2-F -Ph -Ph -C6H4-2-F -C6H4-2-F -C6H4-2-F -C6H4-2-F -C6H4-2-F -Ph -C6H4-2-F -C6H4-2-F -C6H4-2-Cl -Ph -C6H4-2-Cl -Ph -C6H4-2-F
-NO2 -H -Cl -Cl -Cl -Cl -NO2 -Cl -H -H -H -Cl -Cl -Cl -Cl -Cl -Cl -Cl -Cl -H -H -Cl -Cl
-8-SMe -8-F -9-F -8-Cl,9-F -8-CF3 -8-NO2 -8-Cl -8-Cl
A.17 A.18 A.18 A.18 A.18 A.18 A.18 A.19 A.20 A.20 A.20 A.20 A.20 A.20 A.21 A.22 A.22 A.22 A.22 A.23 A.23 A.23 A.23 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24 A.24
0.025 0.41 0.042 0.019 0.0065 0.0056 0.005 0.0244 0.0015 0.0025 0.0042 0.016 0.015 0.23 0.075 0.011 0.004 0.0028 0.0028 0.42 0.0052 0.011 0.0019 >1 3 0.0064 0.0017 0.062 0.046 0.01 0.0032 0.0032 0.0034 0.0062 0.0077 0.0031 0.0033 0.0028 0.0014 0.0025
1 2 1 1 1 2 2 2 2 1 1 1 2 2 2 1 1 2 1 1 1 1 2 3 2 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1
-8-Cl -8-Cl -9-Cl -8-OMe -8-Et -8-Me
Ro16-9906
-OCH2CH=CH2
-8-Cl
A.24
0.0017
2
Ro16-7082 Ro16-7083
-O-i-Bu -O-sec-Bu
-8-Cl -8-Cl
A.24 A.24
0.0063 0.0029
1 1
Ro16-9918
-O-CH2cycloPr
-8-Cl
A.24
0.0023
1
-8-Cl
A.24
0.004
1
-8-Cl
A.24 A.25 A.25 A.25 A.25 A.25
0.0053 >1 0.003 0.0027 0.0068 >1
1 3 1 1 2 3
Ro16-6654 Ro17-1302 Ro15-2427 Ro14-7437 Ro15-3505 Ro15-1310 Ro15-1746
-Ocyclohexyl -O-Ph -NH2 -OEt -OEt -OEt -OEt
-7-Cl -8-Cl -9-Cl
S 12 Ro15-3237 -OEt -10-Cl Ro17-9741 -OMe -7-Cl a names are those given in the original reference. b training set, test set and inactive compounds are indicated as 1, 2 and 3.
A.25 A.26
>1 0.0024
3 1
BZR references (1) Haefely, W.; Kyburz, E.; Gerecke, M.; Mohler, H. Recent advances in the molecular pharmacology of benzodiazepine receptors and in the structure-activity relationships of their agonists and antagonists. Adv. Drug Res. 1985, 14, 165-322.
S 13 COX2 Table A.1.6. Structures (families) of COX-2 inhibitors A.1
A.2
R1
R2
B.1
R1
R2
N
B.2
R1
R2
N
N
R4
R3
C R1
R2
N
R3
B.4
R1
R2
N
R3
B.3
N
N
R3 R4
R1
D.1
R1
R2
R1
R2
N R3 N
N
N
N
R3
R2
R3
D.2
E.1
R3
R3
E.2
F
R1
R1 R2
R1
R2
R1
R3 N
N N
N
R4
n=R3
R2
R3
R3
R2
(CH2)n
G R1
R2
H
I
R1
R1
J.2
R2
N
S
R3
O
R3
K R2
R1
S
N R2
J.1 R2
L
R1
R2
M
R1
R2
R1
R2
R1
N
S
N N
R3
R4
R3
R3
N
N
S 14 Table A.1.7. COX-2 inhibitors a
Name 1-1 1-3 1-4 1-5 1-6 1-8 1-9 1-10 1-16 1-17 1-19 1-20 1-21 1-22 1-27 1-28 1-29 1-31 1-32 1-33 1-34 1-37 1-38 1-41 1-42 2-20 3-5 3-6 3-10 3-12 3-13 3-14 3-15 3-16 3-17 3-18 3-20 3-22 3-27 3-28 3-29 3-30 3-31 3-32 3-33 3-38 3-40 3-41 3-42
R1 -4-SO2Me -4-F -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-F -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2
R2 -4-F -4-SO2Me -4-F -H -4-CF3 -4COMe -3,4-F -4-F -3-SO2Me -4SO2Et -3-Cl-4-SO2Me -4-SO2NH2 -4-SO2NHMe -4-SO2NMe2 -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-Cl -4-Cl -H -4-OMe -4-NHMe -4-NMe2 -4-SMe -4-SOMe -4-SO2Me -4-Cl -H -3-Cl -3-OMe -3-SMe -3-CH2OMe -3-NMe2 -3-NHMe -3-NH2 -3-NO2 -2-Cl -2-Me -2-OMe -2-F
R3 -Me -H -H -Me -Me -Me -Me -Et -H -H -H -H -H -H -CF3 -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3
R4
Family
-H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -COCF3 -COMe -SO2CF3 -CHO -CN -Br -CH2OAc -CH2OH -CH(OH)CF3 -CH2CF3 -H
A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.1 A.2 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1
IC50 (µ µM) 0.06 0.51 10.2 0.06 0.08 2.87 0.25 >100 >100 >100 >100 0.014 >100 >100 >100 0.12 1.61 0.06 3.23 0.75 0.02 0.47 3.88 1.44 0.14 0.52 0.24 0.11 0.12 0.57 1.47 0.7 0.16 >100 5.7 0.01 0.04 0.06 0.35 0.35 68.1 3.2 0.92 5.89 0.58 0.9 0.8 >100 0.1
Set 1 1 2 1 1 2 1 3 3 3 3 2 3 3 3 1 1 2 2 2 2 2 1 1 2 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 2 1 1 1 2 1 1 3 1
b
S 15 3-43 3-44 3-46 3-47 3-49 3-50 3-52 3-54 3-55 3-56 3-57 3-58 3-61 3-64 3-65 3-66 3-69 3-70 3-71 3-72 3-73 3-75
-4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
3-79
-4-SO2Me
3-80
-4-SO2Me
3-83 3-87 3-88 3-89 3-90 3-91 3-92 3-96 3-99 3-100 3-101 3-103 4-25 4-36 4-40 4-41 4-42 4-43 4-44 4-48 4-49 4-58 4-59 4-60 4-62 4-63 4-50 4-51
-4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2Me
-2-Me -4-OMe-3-F -4-SMe-3-Cl -4-NMe2-3-Cl -4-NHMe-3-Cl -4-Me-3-Cl -3-Me-4-F -3-OMe-4-Cl -3-NMe2-4-Cl -3,4-OCH2O-3,4-F -3,4-Me -3-OMe-5-F -2-Me-5-F -2-Me-6-Cl -4-OMe-3-F -4-SMe-3-Cl -4-Me-3-Cl -3-OMe-4-Cl -3,4-F -3-Me-5-Cl -3-OMe-5-Cl -4-OMe-3,5Me -4-OMe-2,5Me -4-Cl 4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -H -2-Me -6-OMe -5-OMe -5-Br -H -2-Me -5-OMe -5-Br -H -H -H -H -H -6-Me -5-Me
-CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 R2 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3
B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1
0.2 0.15 0.04 0.32 0.66 0.03 0.17 0.25 1.04 0.17 0.12 0.33 0.96 >100 >100 0.03 0.01 0.003 0.02 0.03 0.04 0.46
1 1 1 1 2 1 1 1 1 1 1 1 1 3 3 1 1 1 1 1 1 2
-CF3
B.1
0.72
1
-CF3
B.1
12.2
2
-H -CHF2 -CH2F -CHO -CN -CO2Et -CO2H -Ph -CH2OMe -CH2OH -CH2SMe -CH2CN -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CHF2 -CN -Me -CH2OH -CHF2 -CF3 -CF3
B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.1 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.2 B.3 B.3
>100 0.61 0.41 1.6 0.23 5.7 >100 0.24 3.72 8.35 0.32 1.54 1.69 9.6 1.2 37.6 0.95 0.44 2.8 >100 0.34 20.7 24.4 79 93.4 1.83 2.9 1.3
3 1 1 1 1 2 3 1 1 1 2 2 1 1 1 1 1 1 1 3 1 1 2 2 1 2 1 1
S 16 4-52 4-53 4-54 4-55 4-56 4-57
-4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
-4-Me -3-Me -6-Me -5-Me -4-Me -3-Me
4-64
-4-SO2Me
-CF3
-CF3 -CF3 -CF3 -CF3 -CF3 -CF3 N
B.3 B.3 B.3 B.3 B.3 B.3
0.53 5.8 0.42 0.73 0.44 1.54
1 1 1 1 1 1
B.4
1.2
1
B.4
0.63
1
B.4
1.1
2
B.4
0.47
2
B.4 B.4 B.4 B.4 B.4
51 0.47 0.07 0.026 1.1
2 1 1 1 2
B.4
0.94
1
B.4
0.52
1
B.4
0.43
2
B.4
0.11
1
B.4
4.15
2
B.4
0.41
2
C C C C C C C C C C C C
0.026 0.005 0.003 0.865 0.053 77.9 3.2 6.6 0.221 0.075 0.015 0.067
1 1 1 1 2 2 1 2 1 1 1 1
N
4-66
-4-SO2Me
-CF3 H3C N
4-67
-4-SO2Me
-CF3 O
4-69
-4-SO2Me
-CF3
4-70 4-71 4-72 4-73 4-74
-4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2Me
-CF3 -CF3 -CF3 -CF3 -CF3
4-75
-4-SO2Me
O
-3-thienyl -2-thienyl -2-thienyl -4-Br-2-thienyl -3-Me-2-thienyl S
-CF3
CH3 N
S
4-76
-4-SO2NH2
-CF3
CH3 N S
4-77
-4-SO2NH2
N
4-78
-4-SO2NH2 -4-SO2Me
N CH3
-CF3 S
4-79
CH3
-CF3
O
-CF3 N
N
4-80
-4-SO2NH2
-CF3
5-1a 5-1b 5-1d 5-1f 5-1g 5-1h 5-1i 5-1j 5-1k 5-1l 5-7a 5-7c
-4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me
-4-F -4-OMe -4-Me -4-CF3 -2,4-Cl -4-CN -4-CH2OH -4-CH2OCH3 -4-SMe -4-F-2-Me -4-F -4-F
CH3
O CH3
-H -H -H -H -H -H -H -H -H -H -Me -CF3
S 17 5-7e 6-7b 6-7d 6-7i 6-7l 6-7m 6-7p 6-8a 6-8b 6-8h 6-8i 6-8l 6-8m 6-8o 6-8p 7-16a 7-16d 7-17a 7-17b 7-17d 7-20c 7-20f 7-20g 7-20h 7-20i 7-20j 7-20k 7-20o 7-21c 7-21d 7-21g 7-21h 7-21i 7-21j 7-21l 7-21m 7-21o 7-32 7-34 7-36 7-20q 7-21q 7-20p 7-21p 8-1b 8-1c 8-1d 8-1g 8-1i 8-1j 8-1l 8-1m 8-1n
-4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
-4-F -3,4-F -3-CF3-4-F -4-OMe-3-F -3,4-OCH2O-4-NMe2-3-Cl -4-CF3-3-F -4-F -3,4-F -4-OMe -4-OMe-3-F -3,4-OCH2O-4-NMe2-3-Cl -4-CF3 -4-CF3-3-F -4-F -4-OMe-3-F -4-F -4-F-3-Cl -4-OMe-3-F -4-F-3-Me -4-OMe-3,5-Cl -4-OMe-3-Me -3,4-OMe -3,4-OEtO-3,4-OMeO-4-Me -4-NMe2-3-Cl -4-F-3-Me -4-OMe-3-F -4-OMe-3-Me -3,4-OMe -3,4-OEtO-3,4-OMeO-4-Me-3-Cl -3,4-Me -4-NMe2-3-Cl -4-F -4-F -4-F -6-Me-3-pyridyl -6-Me-3-pyridyl -5-Me-2-pyridyl -5-Me-2-pyridyl
-2-F -3-F -4-F -2-Me -4-Me -4-Et -4-NO2 -4-OH -2-OMe
-CH2F -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-F -3,4-OMeO-2,3,4,5-F -3,4-(CH)4-3,4-F -3,4-F -3,4-F -3,4-F -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3
-H -H -H -H -H -H -H -H -H
C C C C C C C C C C C C C C C D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.1 D.2 D.2 D.2 D.2 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1
0.051 0.051 >100 0.12 0.021 0.005 0.76 0.007 0.018 0.002 0.016 0.002 0.002 0.15 0.17 0.26 >100 0.061 0.017 0.033 0.005 >100 0.013 0.34 0.34 0.012 0.007 0.008 0.002 0.013 0.005 0.065 0.032 0.004 0.003 0.005 0.006 0.083 >100 >100 0.17 0.051 52.3 0.33 0.058 7.73 0.041 0.069 0.04 0.86 2.63 >100 0.29
2 1 3 1 1 2 1 1 1 2 1 2 1 1 2 2 3 1 1 2 1 3 2 1 1 1 1 1 1 1 1 2 2 1 1 2 2 2 3 3 2 1 2 1 1 1 1 1 1 1 1 3 1
S 18 8-1o 8-1p 8-1q 8-1r 8-1s 8-1t 8-1u 8-1v 8-1w 8-1x 8-1y 8-1z 8-1aa 8-1ab 8-1ac
-4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
8-1ad
-4-SO2NH2
8-1ae 8-1af 8-1ag 8-2a 8-29 8-2c 8-2d 8-2e 8-2f 8-2g 8-2h 8-2l 8-2o 8-3a 8-8a 8-9b 8-10a 8-11a 8-13a 8-14a 8-16a 8-17a 8-19 8-20b 8-20c 8-20d 8-20e 8-20f 8-20g 8-21b 8-22a 8-22c 8-22d 8-22e 8-22f 8-23 8-24
-4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NHCH3
-4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
-4-OMe -4-OEt -4-SMe -4-NH2 -2-NMe2 -4-NHMe -4-NMe2 -4-CH2OH -4-CO2H -4-OMe-3-Me -4-OMe-3-Et -3,4-OMe -3-Me-4-SMe -3-F-4-NMe2 -4NHMe-3-Cl -5-Me-4-OMe3-Cl -3,4-Cl -2,4-Cl -2,5-Cl -4-Cl -4-Cl -4-CN -4-SO2Me -4-CONH2 -4-CO2H -4-OMe -4-OMe-3-F -2,5-Me -H -4-F -H -4-Cl -4-F -4-F -4-F -4-Cl -H -4-Cl -H -H -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-Cl -4-F -H -4-Me -H -4-Cl -H -H
-CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3
-H -H -H -H -H -H -H -H -H -H -H -H -H -H -H
E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1
0.008 0.64 0.009 0.34 14.3 0.016 0.0047 93.3 11.2 0.0093 0.43 0.6 0.0037 0.0057 0.027
1 2 1 1 2 1 1 2 1 1 1 1 1 1 2
-CF3
-H
E.1
0.066
1
-CF3 -CF3 -CF3 -CHF2 -CF3 -CHF2 -CHF2 -CHF2 -CHF2 -CHF2 -CHF2 -CHF2 -CHF2 -CO2Me -Me -5-Cl-2-thienyl -CO2H -CO2NH2 -CN -CH2OH -CH2F -CH2CN -OMe -Me -CH2OH -CN -CO2H -CO2Me -CONH2 -H -H -H -H -H -H -H -CF3
-H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -H -Cl -Cl -Cl -Cl -Cl -Cl -Br -H -Me -CN -NO2 -SO2Me -NH2 -F
E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1
0.015 0.056 >100 0.01 >100 29.7 >100 >100 46.8 0.015 0.05 >100 0.13 100 62.8 0.052 >100 >100 0.34 0.83 0.2 0.12 >100 0.028 0.34 0.01 70 0.16 1.09 0.031 >100 47.1 0.076 0.29 19.8 29.7 0.0017
1 1 3 1 3 2 3 3 2 1 1 3 1 3 2 2 3 3 2 2 1 2 3 1 1 1 2 2 2 2 3 2 2 2 2 2 1
S 19 8-25a 8-25b 8-25d 8-26 8-28a 8-30 8-31
-4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-F -4SO2N(CH3)2 -4NHSO2CH3 -4-NO2 -4-COCF3 -H -4-Cl -4-OMe -4-Cl -4-OMe -4-SO2Me
-4-Cl -4-Cl -H -H -4-SO2NH2
-CF3 -CF3 -CF3 -CF3 -CF3
-Me -Et -OMe -OH -H
E.1 E.1 E.1 E.1 E.1
0.022 0.028 0.08 3.58 0.01
1 2 2 1 1
-4-Cl
-CF3
-H
E.1
>100
3
-4-Cl
-CF3
-H
E.1
>100
3
-4-Cl -4-Cl -H -4-Cl -4-OMe -4-OMe -4-Cl -4-F
-CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3 -CF3
-H -H -H -H -H -H -H -H
E.1 E.1 E.1 E.1 E.1 E.1 E.1 E.1
>100 >100 >100 4.79 0.75 0.75 74.9 0.1
3 3 3 1 1 2 2 2
-H
E.1
0.04
1
E.2 E.2 E.2 E.2
45.6 45 64.7 0.012
2 2 2 1
E.2
0.35
2
E.2
0.89
2
E.2
0.084
2
E.2
0.031
2
E.2
0.23
1
E.2
0.021
1
E.2
0.052
1
E.2
3.29
1
E.2
0.024
2
F F F F F F F
0.0075 0.017 0.002 0.003 0.0015 0.005 0.001
1 2 1 2 1 1 1
8-32 8-33 8-34 8-35 8-36 8-37 8-38 8-39 8celecoxib 8-1ai 8-1aj 8-1ak 8-1al
-4-SO2NH2
-4-Me
-CF3
-4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2
-CF3 -CF3 -CF3 -CF3
-2-pyridyl -3-pyridyl -4-pyridyl -thienyl-5-Br
8-1an
-4-SO2NH2
-CF3 S
8-1ao
-4-SO2NH2
-CF3 O
8-1ap
-4-SO2NH2
-CF3
8-1aq
-4-SO2NH2
-CF3
8-1ar
-4-SO2NH2
-CF3
-1-cyclohexene
S
8-1as
-4-SO2NH2
-CF3 O
O
8-1at
-4-SO2NH2
-CF3
8-2m
-4-SO2NH2
-CHF2
O CH3
-furyl-5-Me O
8-2n
-4-SO2NH2
-CHF2 O
9-3 9-20 9-24 9-32 9-35 9-36 9-37
-4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2NH2
-4-F -4-OMe-3-Cl -4-OMe-3-Cl -4-F -4-Me -4-OMe -4-OMe
0 0 0 0 0 0 0
S 20 9-38 9-39 9-40 9-41 9-46 9-47 9-48 9-53 9-19 9-29 10-2 10-3 6-Dup697 11-8 11-10 11-13 11-14 11-16 11-21 11-24 11-25 11-26 11-29 11-30 11-31 11-32 12-3a 12-5a 12-5b 12-10b 12-10c 11-33 11-34 13-4 13-5
-4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-F -4-F -4-F -4-F -4-F -4-F -4-F -4-F -2-F -3-F -2,5-F -2,4-F -4-F -H -4-Cl -4-OMe-3-F -4-OMe-3-F -2-thienyl -3-thienyl -4-SO2Me -4-SO2Me
-4-OCF3 -4-OCF3 -4-CF3 -4-CF3 -3,4-OCH2O-3,4-F -3,4-F -2,4-F -4-F -4-OCH3-3-Cl -Me -CH2OH -4-F -4-F -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2Me -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2NH2 -4-SO2Me -4-SO2Me -4-F -4-F
0 0 0 0 0 0 0 0
-Br -Me -CF3 -Et -t-Bu -CH2CN -C6H4-2-Cl -2-thienyl -3-pyridyl -4-pyridyl -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-Cl -C6H4-2-Cl -CH3 -CH3 -C6H4-2-Cl -Me -C6H4-2-Cl -C6H4-2-Cl -H -CF3
13-6a
-4-SO2Me
-4-F
-H
13-7a
-4-SO2Me
-4-F
-CF3
-H -H CH2CH=CH2 CH2CH=CH2 -Et -Et
F F F F F F F F G G H H I J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.2 J.2 K K
0.135 0.13 0.002 0.001 0.0025 0.0033 0.003 0.022 0.026 0.027 0.005 0.18 0.01 0.12 0.023 0.023 0.11 0.35 0.05 0.021 0.43 1.6 0.01 0.016 >100 0.021 0.013 0.038 0.005 2.48 0.028 0.057 0.079 >100 >100
1 1 2 1 1 1 1 1 2 1 1 2 2 1 1 1 1 2 1 1 1 1 2 1 3 1 1 1 1 2 2 1 2 3 3
K
>100
3
K
0.075
2
13-7c -4-SO2Me -4-F -CF3 K 0.13 13-10 -4-SO2NH2 -4-F -CF3 K 0.033 14-3 -4-SO2Me -4-F C L 0.011 14-7 -4-SO2Me -4-F O L 0.02 14-13 -4-SO2NH2 -4-F C L 0.005 14-12 -4-SO2NH2 -4-F O L 0.007 14-14 -4-SO2Me -3-F-4-OMe O L 0.093 14-15 -4-SO2NH2 -3-F-4-OMe O L 0.005 7-39 -4-SO2Me -4-F M >100 a names are formed by hyphenating the reference number and the label given to the compound in the reference. b training set, test set and inactive compounds are indicated as 1, 2 and 3.
1 1 2 1 1 2 2 1 3
S 21 COX-2 references (1) Khanna, I. K.; Weier, R. M.; Yu, Y.; Collins, P. W.; Miyashiro, J. M. et al. 1,2-diarylpyrroles as potent and selective inhibitors of cyclooxygenase-2. J. Med. Chem. 1997, 40, 1619-1633. (2) Chavatte, P.; Yous, S.; Marot, C.; Baurin, N.; Lesieur, D. Three-dimensional quantitative structure-activity relationships of cyclo-oxygenase-2 (cox-2) inhibitors: A comparative molecular field analysis. J. Med. Chem. 2001, 44, 3223-3230. (3) Khanna, I. K.; Weier, R. M.; Yu, Y.; Xu, X. D.; Koszyk, F. J. et al. 1,2-diarylimidazoles as potent, cyclooxygenase-2 selective, and orally active antiinflammatory agents. J. Med. Chem. 1997, 40, 1634-1647. (4) Khanna, I. K.; Yu, Y.; Huff, R. M.; Weier, R. M.; Xu, X. D. et al. Selective cyclooxygenase-2 inhibitors: Heteroaryl modified 1,2-diarylimidazoles are potent, orally active antiinflammatory agents. J. Med. Chem. 2000, 43, 3168-3185. (5) Reitz, D. B.; Li, J. J.; Norton, M. B.; Reinhard, E. J.; Collins, J. T. et al. Selective cyclooxygenase inhibitors novel 1,2-diarylcyclopentenes are potent and orally-active COX-2 inhibitors. J. Med. Chem. 1994, 37, 38783881. (6) Li, J. J.; Anderson, G. D.; Burton, E. G.; Cogburn, J. N.; Collins, J. T. et al. 1,2-diarylcyclopentenes as selective cyclooxygenase-2 inhibitors and orally-active antiinflammatory agents. J. Med. Chem. 1995, 38, 4570-4578. (7) Li, J. J.; Norton, M. B.; Reinhard, E. J.; Anderson, G. D.; Gregory, S. A. et al. Novel terphenyls as selective cyclooxygenase-2 inhibitors and orally active anti-inflammatory agents. J. Med. Chem. 1996, 39, 1846-1856. (8) Penning, T. D.; Talley, J. J.; Bertenshaw, S. R.; Carter, J. S.; Collins, P. W. et al. Synthesis and biological evaluation of the 1,5-diarylpyrazole class of cyclooxygenase-2 inhibitors: Identification of 4-[5-(4methylphenyl)-3-(trifluoromethyl)-1h-pyrazol-1-yl]benzenesulfonamide (SC-58635, Celecoxib). J. Med. Chem. 1997, 40, 1347-1365. (9) Huang, H. C.; Li, J. J.; Garland, D. J.; Chamberlain, T. S.; Reinhard, E. J. et al. Diarylspiro[2,4]heptenes as orally active, highly selective cyclooxygenase-2 inhibitors: Synthesis and structure-activity relationships. J. Med. Chem. 1996, 39, 253-266. (10) Talley, J. J.; Brown, D. L.; Carter, J. S.; Graneto, M. J.; Koboldt, C. M. et al. 4-[5-methyl-3-phenylisoxazol-4yl]-benzenesulfonamide, Valdecoxib: A potent and selective inhibitor of COX-2. J. Med. Chem. 2000, 43, 775777. (11) Carter, J. S.; Rogier, D. J.; Graneto, M. J.; Seibert, K.; Koboldt, C. M. et al. Design and synthesis of sulfonylsubstituted 4,5-diarylthiazoles as selective cyclooxygenase-2 inhibitors. Bioorg. Med. Chem. Lett. 1999, 9, 1167-1170. (12) Carter, J. S.; Kramer, S.; Talley, J. J.; Penning, T.; Collins, P. et al. Synthesis and activity of sulfonamidesubstituted 4,5-diaryl thiazoles as selective cyclooxygenase-2 inhibitors. Bioorg. Med. Chem. Lett. 1999, 9, 1171-1174. (13) Penning, T. D.; Kramer, S. W.; Lee, L. F.; Collins, P. W.; Koboldt, C. M. et al. 3,4-diarylpyrazoles: Potent and selective inhibitors of cyclooxygenase-2. Bioorg. Med. Chem. Lett. 1997, 7, 2121-2124. (14) Huang, H. C.; Chamberlain, T. S.; Seibert, K.; Koboldt, C. M.; Isakson, P. C. et al. Diaryl indenes and benzofurans - novel classes of potent and selective cyclooxygenase-2 inhibitors. Bioorg. Med. Chem. Lett. 1995, 5, 2377-2380.
S 22 DHFR Table A.1.8. Structures (families) of DHFR inhibitors E
F.1 N
N
G.1
O
NH2
R1
H2N
I.1
NH2 R1
N H2 N NH2
R1 N
K
N
NH2
L
R3 R2
N H2N
N
H2N
N H
N.1
O
NH2 N
N H 2N
R1 N
N H
N
NH2 N
N
R2 R1
N
N.3 O
R1
R2 N
N
R2 N
R1
N N
H2N
N H H2N
H2N
R3
H2N
M
R1 N
N
N
N
R1
NH2
R2
R1
N
R2
N
N
J.3
R3
R2
N H2N
N
NH2
N.2 NH2
NH2
R1
N
R1
R1
H2N
H2 N
R2
R2
R2
N
N
N
H2N
R3
N
NH2
R1
N
R1
R2
N H2N
N
N
NH2
I.2
J.2
R3
R2
NH2
H2N
N
H.1
R1
N
N
N
N H2N
N
R1
H.2
R2
N NH2
R2
N
J.1
N
H2N
NH2
R1
G.2
R3
N H2N
N
N N
H2N
F.2
NH2
NH2
R3
H 2N
N
N H
R1
S 23 Table A.1.9. DHFR inhibitors
7-1 7-2 7-3 7-4 7-5 7-6 1-98535 1-107146 1-117356 1-127977 1-131463 1-137545 1-144698 1-152737 1-233903 1-233904 1-233910 1-235791 1-236642 1-241522 9-12c 9-12d 9-12e 9-12g 9-12h 9-12i 9-12j 9-12k 9-12l 9-12m 9-12n 9-12o 9-12p 9-12q 9-12r 9-12s 9-12t 9-12u 10-2d 9-12f 1-232965 1-235776 1-233912 1-235777 6-48 11-GR92754
R1 -H -3,4,5-OMe -3,5-OMe -2,4-Cl -3,4-Cl -2,6-Cl -4-CO-L-Glu -2-F,-4-D-Glu -4-D-Glu -4-CO-D-Lys -4-CO2H -2-Me,-4-CO2H,-6Me -2-CF3,-4-D-Glu -2-OMe,-4-D-Glu -4-CONH2 -H -4-NHCOMe -4-COMe -4-CON(Me)2 -4-CONH-Pr -2,3-(CH)4-3-Me -4-Me -4-OMe -3,4-OMe -3-Cl -4-Cl -4-Cl -2-Me,-5-OMe -2-Me,-6-OMe -2,5-OMe -2,5-OMe -3,5-OMe -3,4,5-OMe -2-OMe,-5-CF3 -3-OMe,-5-CF3 -2,3-(CH)4-2,5-OMe -H -3-OMe -CH2-S-Ph -CH2-NH-Ph -CH2-O-Ph -CH2NH-1-naphthyl 1,2-naphthyl -i-Butyl
>9 >35 >22.8 22.6 24.1 40.5 0.028 0.00072 0.00088 >8 0.94
1.4 >35 >20.4 13.1 22.3 31.7
-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-CH2N(Me)-
E E E E E E F.1 F.1 F.1 F.1 F.1
-CH2N(Me)-
F.1
-CH2N(Me)-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2NH-CH2NH-CH2S-CH2S-CH2S-CH2S-CH2S-CH2S-CH2S-CH2NH-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2NH-CH2NH-CH2CH2-CH2CH2-CH2CO2-CH2S-H -H -H -H R1 -R1
F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.1 F.2 F.2 F.2 F.2 F.2 F.2
R3
TG
c
PC
R2
b
RL
Set
Name
IC50 (µ µM)
Family
a
>8 2.27
15 >35 22.8 50.9 20.6 81.2 0.017 0.00036 0.0062 >8 0.11
2 3 2 1 1 2 1 1 1 3 1
0.19
0.28
0.038
2
0.00031 0.00049 >1000 10 7.1 0.72 >5 3.1 4.2 21.2 30 17.2 58.2 42.2 42.1 1.5 >3 15.8 6.2 3.9 0.96 7 21 0.68 97 11.1 9.8 9.9 9.5 >1.9 136 0.13 18.4 0.082
0.0067
0.00155 0.0011 220 0.83 0.17 0.075 >10 0.48 8.2 8.48 26 10.2 36.3 26.6 14.3 0.3 >3 5.7 22.9 0.47 0.88 1.9 21 1.9 60 23.2 7 7.7 246 >1.9 13 1.26 1.3 0.32
1 2 1 1 2 1 3 2 1 1 1 1 2 1 1 1 3 1 1 2 1 1 1 2 2 2 2 1 1 3 2 1 2 1
0.0119
16.9
7 1.8 15 14 23.2 5.7 16.8 0.59 0.44 1.85 6.9 0.21 0.11 1 10.6 0.89 0.82 5.4 5.8 1.6 0.77 2.7 2.7 0.076 4.9 0.028
S 24 11-AH2503 11-AH2504 12-4b
12-4d
-Et -C6H4-2-OMe N
N
-R1 -Et
F.2 F.2
0.62 2
1 0.018
2.2 0.41
2 2
-H
F.2
1.4
0.91
5.1
1
-H
F.2
3.4
2.2
13
1
-H
F.2
4.9
1.3
4
2
-H
F.2
0.042
0.029
0.027
1
-H
F.2
0.12
0.11
0.2
2
-H
F.2
0.21
0.043
4.4
1
O
12-4g 12-4c
12-4e
-CH2N(Ph)2 N
N
S
12-4a 10-18d 1-122870 1Trimetrexate 1-184692 1-351521 13-10 13-11 13-14 13-17 14-28 14-29 9-16b 9-16c 15-3 15-4 15-5 15-6 15-7 15-10 10-1a 10-3a 10-4a 10-5a 10-6a 16-9a 16-11 15-11 15-12 15-13 15-14 15-15 10-11a
N
-CH2OH -4-CO-L-Asp
-H -CH2NH-
-Me
F.2 G.1
>51 0.00042
>51 0.00133
>51 0.000156
3 1
-3,4,5-OMe
-CH2NH-
-Me
G.1
0.042
10
0.003
2
-4-CO-L-Asp -3,5-OMe -3,4,5-OMe -2,5-OMe -3,4,5-OMe -3,4,5-OMe -2,5-OMe -3,4,5-OMe -4-Cl -2-Me,-4-Cl -2,5-OMe -3,5-OMe -2,4-OMe -3,4,5-OMe -2,3,4-OMe -2,3-(CH)4-H -3,4,5-OMe -2,5-OMe -2,3,4-OMe -3,5-OMe -2-Br,-3,4,5-OMe -2-Br,-3,4,5-OMe -2,5-OMe -3,5-OMe -2,4-OMe -2,3,4-OMe -2,3-(CH)4-H
-CH2NH-CH2-CH2N(Me)-NHCH2-NHCH2-N(Me)CH2-CH2NH-CH2NH-CH2NH-CH2NH-NHCH2-NHCH2-NHCH2-NHCH2-NHCH2-NHCH2-CO2CH2-CH2CO2-CH2CO2-CH2CO2-CH2CO2-CH2NH-CH2NH-N(Me)CH2-N(Me)CH2-N(Me)CH2-N(Me)CH2-N(Me)CH2-CH2NH-
-Et -Me -Cl -Cl -Cl -Cl -Cl -Cl -H -H -H -H -H -H -H -H -H -H -H -H -H -Cl -H -H -H -H -H -H -H
G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1 G.1
0.010 0.031 0.012 0.053 0.033 0.17 0.051 0.033 0.6 0.33 4.6 2.2 4.4 6.8 4.9 0.72 2.5 0.56 2.4 1.4 0.46 0.028 0.55 0.087 0.024 0.1 0.052 0.017 0.98
0.001
0.004 0.002 0.012 0.028 0.006 0.038 0.044 0.006 0.073 0.023 1.1 0.84 1.2 0.9 1.3 0.19 0.42 0.026 0.42 0.5 0.35 0.010 0.33 0.026 0.008 0.043 0.019 0.017 0.44
2 2 1 2 1 1 1 1 1 2 1 1 1 1 1 1 2 2 1 1 1 2 1 1 2 1 1 1 1
0.006 0.017 0.007 0.016 0.03 0.005 0.075 0.033 0.16 0.12 0.17 0.084 0.19 0.099 0.36 0.05 0.22 0.14 0.15 0.008 0.039 0.03 0.009 0.039 0.017 0.021 0.1
S 25 10-12a 6-1 6-2 6-3 6-7 6-13 6-14 6-15 6-16 6-20 6-21 6-22 6-23 6-26 6-28
-H -Me -CF3 -F -OMe -SMe -H -H -H -H -H -H -H -Cl -H
-CH2N(Me)-H -H -H -H -H -Me -CF3 -F -OMe -H -H -H -Cl -Me
7.7
0.069 7.4 215 5 1.2 0.54 55 4.1 452 46 42 63 189 3.5 7.9
2 1 2 2 1 2 1 1 1 2 1 1 1 1 2
13
5.8
1.5
2
G.2
0.51
0.13
0.019
2
G.2 G.2 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1 H.1
>32 51.7 4.6 0.095 0.119 1.67 0.3 0.114 1.57 0.319 6.8 0.246 0.41 0.502 0.94 0.171 0.33 0.517 0.1 0.29 0.25 0.34 0.45 0.27 0.44 0.4 0.1 0.58 0.057 0.1
>32 44.9 0.054 0.007 0.012 0.181 0.015 0.017 0.14 0.017 0.11 0.021 0.097 0.010 0.078 0.022 0.03 0.036 0.023 0.032 0.023 0.036 0.014 0.021 0.05 0.14 0.014 0.073 0.021 0.023
>32 40.3 0.29 0.038 0.074 0.56 0.26 0.071 1.47 0.116 0.15 0.034 0.24 0.109 0.128 0.067 0.227 0.139 0.047 0.18 0.11 0.11 0.12 0.11 0.077 0.19 0.079 0.17 0.034 0.063
3 1 1 1 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1
-H -H -H -H -H -H -H -H -H -H -Me -CF3 -F -H -Me
G.1 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2 G.2
0.096 1.5 82 0.41 4.5 1.1 20 2.7 119 58 65 31 41 9.7 5.3
-H
G.2
-H -H -H
0.011 4.98
0.48
3.1 104 22 81
NH
18-5
-H NH
18-6
-H
10-17a 10-18a 19-1 19-2 19-3 19-4 19-5 19-6 19-7 19-8 19-9 19-10 19-11 19-12 19-13 19-14 19-15 19-19 19-20 20-5a 20-5b 20-5c 20-5d 20-5e 20-5f 20-5g 20-5h 20-5i 20-5j 20-5k
-H -H -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -2,5-OMe -2,5-OMe -2,5-OMe -2,5-OEt -2,5-OEt -3,4-Cl -3,4-Cl -2,5-Cl -2,6-Cl -4-Cl -4-Cl -3-Br -2,3-(CH)4-2,3-(CH)4-H -2-Me -3-Me -2-OMe -3-OMe -4-OMe -3-CF3 -3-OCF3 -4-OCF3 -2,5-OMe -3,4-OMe
-CO2H -CH2OH -CH2NH-CH2N(Me)-CH2N(CH2C≡CH)-CH2NH-CH2N(Me)-CH2N(Et)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2N(Me)-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-
S 26 20-5m 20-9a 20-9b 20-9c 14-5 14-8 14-9 14-10 21-3 21-4 21-5 21-6 21-7 21-8 21-9 21-10 21-11 21-12 21-13 21-14 21-15 21-16 21-18 21-19 21-20 21-21 21-22 21-23 21-24 21-27 21-34 21-36 21-38 21-40 21-41 21-42 21-43 21-44 22-4 22-5 22-6 22-7 22-8 22-9 22-11 22-12 22-15 22-19 22-21 22-14 22-20 22-16 22-22
-3,4-Cl -Et -t-Bu -Ph -2,5-OMe -4-Cl -3-Cl -3,4-Cl -H -H -H -2-OMe -2-OMe -3-OMe -3-OMe -4-OMe -4-OMe -2-Cl -2-Cl -3-Cl -2,4-OMe -2,4-OMe -2,5-OMe -3,4-OMe -3,4-OMe -2,4-Cl -2,4-Cl -2,5-Cl -2,5-Cl -3,4-Cl -2,3-(CH)4-2,3-(CH)4-2,3-(CH)4-4-COMe -4-COMe -4-COMe -4-COCF3 -4-COCF3 -2-OMe -4-OMe -3,4-OMe -2-OMe -4-OMe -3,4-OMe -2-OMe -4-OMe -3,4-OMe -4-OMe -3,4-OMe -2,5-OMe -2,5-OMe -3,4,5-OMe -3,4,5-OMe
-CH2-
-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-CH2S-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2NH-CH2S-CH2NH-CH2N(Me)-CH2NH-CH2N(Me)-CH2N(C≡CH)-CH2N(Me)-CH2N(C≡CH)-S-S-S-SO2-SO2-SO2-NH-NH-NH-N(Me)-N(Me)-NH-N(Me)-NH-N(Me)-
H.1 H.2 H.2 H.2 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1 I.1
15 6.9 0.18 2.2 1.4 0.062 2.1 0.022 2 1.7 0.29 2.7 0.51 1.7 0.097 0.85 0.25 0.53 0.21 2 5.5 0.16 0.21 0.9 0.091 0.73 0.5 1.6 0.15 0.41 0.47 0.23 0.04 0.41 0.13 0.22 0.25 0.12 2.2 0.7 0.086 3.2 10.5 2.7 8.7 90.4 40.4 0.22 0.0023 16.1 0.034 25.9 0.021
2.6 1.1 0.018 1.3 0.1 0.015 0.02 0.098 0.13 0.085 0.008 0.12 0.026 0.1 0.015 0.054 0.016 0.11 0.015 0.13 0.14 0.014 0.025 0.09 0.010 0.05 0.05 0.091 0.025 0.057 0.049 0.026 0.018 0.027 0.015 0.02 0.046 0.054 0.058 0.045 0.019 0.21 1 0.94 0.46 2.8 0.68 0.009 0.00088 0.73 0.041 2.4 0.007
7.3 3 0.065 1.9 0.43 0.022 0.067 0.032 0.52 0.26 0.024 0.42 0.12 0.2 0.035 0.073 0.018 0.14 0.12 0.14 0.32 0.016 0.05 0.06 0.003 0.088 0.058 0.2 0.047 0.054 0.16 0.04 0.007 0.003 0.005 0.015 0.032 0.008 0.23 0.075 0.018 1.4 2 0.88 0.26 3.8 1.1 0.007 0.0004 3.6 0.004 3.2 0.004
1 1 1 2 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 2 1 1 2 1 1 1 1 2 1 1 1 2 1 1 1 2 2 1 2 1 1
S 27 22-23 22-17 22-10 22-18 22-13 22-25 18-4 8-3 8-6 8-7 8-8 23-6a 23-4b 23-6b 24-2a 24-2b 24-2c 24-2d 24-2e 24-3a 24-3c 24-3e 24-4a 24-4c 24-5a 24-5b 14-22 9-13b 9-13d 9-13e 9-13f 9-13g 9-13h 9-13i 9-13j 9-13l 9-13m 9-13r 9-13s 9-13t 9-13u 9-14a 9-14b 9-14c 9-14h 9-14k 9-14m 9-15a 9-15b 9-15c 9-16d
-2,3-(CH)4-3,4-(CH)4-H -H -4-Cl -3,4,5-OMe
-N(Me)-NH-NH-N(Me)-NH-NHCH2-
N
-H -2,5-Cl -3,5-Cl -3,4-OMe -3,4,5-OMe -3,4-Cl -3,4-Cl -2,5-OMe -3,5-OMe -2,4-OMe -3,4-OMe -2,5-OEt -2,5-OMe -2,4-OMe -2,5-OEt -3,4,5-OMe -3,4,5-OMe -2,3-(CH)4-2,3-(CH)4-,-4-OMe -3,4-Cl -H -3-Me -4-Me -3-OMe -4-OMe -3,4-OMe -3-Cl -4-Cl -2-Me,5-OMe -2-Me,-6-OMe -2-OMe,-5-CF3 -3-OMe,-5-CF3 -2,3-(CH)4-2,5-OMe -2,5-Me -2-Me,-4-OMe -2-OMe,-5-Me -3,4-OMe -2-OMe,-5-CF3 -2,3-(CH)4-2,3-(CH)4-4-Cl -3,4,5-OMe -2,5-OMe
-CH2S-CH2S-CH2S-CH2S-CH2N(CHO)-CH2NH-CH2N(CHO)-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-CH2N(CH2C≡CH)-CH2N(Et)-CH2NH-CH2NH-CH2N(Me)-CH2S-CH2S-CH2S-CH2S-CH2S-CH2S-CH2S-CH2S-CH2NH-CH2NH-CH2NH-CH2NH-CH2CH2-CH2CH2-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-CH2NH-CH2NH-CH2NH-CH2NH-
-H -H -H -H -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -H -H -H -H
I.1 I.1 I.1 I.1 I.1 I.1
5.1 15 8.3 0.010 14.6 29.4
2.1 1.1 0.3 0.002 0.83 0.49
3.3 2 0.43 0.001 0.82 1.4
1 2 1 1 1 2
I.2
0.037
0.034
0.053
2
J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1
1.3 5.9 11 2.2 0.55 0.32 0.51 0.046 0.023 0.316 0.044 0.077 0.216 0.32 3.1 0.054 0.050 0.573 0.041 0.1 0.44 0.17 0.53 0.34 0.56 0.15 0.068 0.36 0.038 1 0.044 0.02 0.064 0.34 0.03 0.17 0.068 0.32 0.093 0.15 0.26 0.97 2 0.75
0.47 2 6.2 1.1 0.013 0.028 0.083 0.016 0.005 0.057 0.009 0.017 0.030 0.029 0.1 0.008 0.003 0.015 0.023 0.027 0.034 0.065 0.057 0.11 0.063 0.03 0.09 0.09 0.023 0.1 0.022 0.018 0.026 0.008 0.016 0.007 0.015 0.003 0.038 0.016 0.15 0.3 0.13 0.14
1.9 2.5 38 4 0.11 0.053 0.14 0.128 0.043 0.214 0.008 0.017 0.407 0.044 3.0 0.012 0.011 0.030 0.054 0.042 0.43 0.33 0.5 0.6 0.52 0.18 0.19 0.37 0.15 0.32 0.02 0.017 0.135 0.77 0.12 0.029 0.16 0.004 0.23 0.14 0.23 0.72 0.81 0.46
1 1 2 2 2 1 2 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 2 1 1 1
S 28 25-10 25-11 25-12 25-13 25-14 25-15 25-16 25-19 25-20 25-21 25-22 25-23 25-24 25-25 25-26 26-7 26-8 26-9 26-10 27-6 27-7 27-9 27-10 27-11 27-13 27-14 27-15 27-16 10-2b 10-2c 28-3 28-4 28-5 28-6 28-7 28-8 28-9 28-10 28-11 29-2-piritrexim 26-5
-H -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -2,3,4-OMe -2,3,4-OMe -2,4,6-OMe -3,5-OMe -3,5-OMe -2,5-OMe -2,5-OMe -2,3-(CH)4-2,3-(CH)4-,-4-OMe -2,3-(CH)4-,-6-OMe -4-O-Ph -2,5-OMe,-4pyrrolo -2-pyrrolo,-4,5OMe -2,3,5,6-OMe,-4pyrrolo -2-OMe,-5-Ph -2-OMe -3-OMe -2-Cl -3-Cl -4-Cl -3-OMe -4-OMe -2-Cl -4-Cl -H -H -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -3,4-OMe -4-OMe -3,4,5-OMe -3,4-OMe -4-OMe -2,5-OMe N
-N(Me)CH2-NHCH2-N(Me)CH2-NHCH(Me)-NHCH2-N(Me)CH2-NHCH2-NHCH2-N(Me)CH2-NHCH2-N(Me)CH2-NHCH2-NHCH2-NHCH2-NHCH2-
-H -H -H -H -H -H -H -H -H -H -H -H -H -H -H
J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1
0.068 14.1 0.061 9.2 15.3 0.079 20.7 5.7 0.076 3.8 0.084 3.9 8.2 15.4 24.3
0.032 0.35 0.014 0.194 0.67 0.026 0.23 1.2 0.031 0.31 0.006 0.98 0.38 0.71 3.7
0.14 3.3 0.033 1.27 3.24 0.03 1.2 3.4 0.072 0.35 0.057 0.24 0.43 0.37 2.9
2 1 1 1 1 2 1 1 1 1 1 1 1 1 2
-CH2NH-
-Me
J.1
0.35
0.033
0.23
2
-CH2NH-
-Me
J.1
1.8
0.6
3.5
1
-CH2NH-
-Me
J.1
0.62
0.075
0.17
2
-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2(Me)-CH2(Me)-CH2(Me)-CH2(Me)-CH2CO2-CH2CO2-CH2N(Me)-CH2N(Et)-CH2N(CHO)-CH=CH-CH=CH-CH=CH-CH2CH2-CH2CH2-CH2CH2-CH2-
-Me -Me -Me -Me -Me -Me -Me -Me -Me -Me -H -Me -H -H -H -H -H -H -H -H -H -Me
J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1 J.1
0.64 0.117 0.069 0.047 0.023 0.055 0.03 0.035 0.084 0.029 5.45 0.25 0.24 0.19 18.5 >5.0 2.6 5.3 5 1.4 0.29 0.031
0.068 0.023 0.007 0.007 0.011 0.019 0.006 0.007 0.018 0.005 1.9 0.056 0.009 0.049 1.1 1.4 1.4 1.5 0.2 0.2 0.25 0.017
0.44 0.169 0.080 0.088 0.037 0.051 0.018 0.013 0.1 0.026 3.9 0.23 0.28 0.12 7.4 12.9 2.1 11.8 1.14 0.61 0.26 0.002
1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 2 2 1 1 1 2 2
-Me
J.2
0.57
0.077
0.47
2
-Me
J.2
0.25
0.057
0.17
1
OMe
30-3
N
OMe
S 29
N
30-2
-Me
J.2
0.29
0.048
0.15
2
-Me
J.2
0.41
0.049
0.23
1
-H
J.2
0.043
0.04
0.19
2
-H -Me -CH2CHO-CH2CHO-CH2NH-CH2CH2-CH2-CH2-CH2-CH2CH2-CH2NH-CH2N(Me)-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-CH2S-CH2S-CH2S-CH2N(Me)-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-
>104 10.5 >2.6 >1.2 >3700 61.7 3.3 6.9 0.51 30 0.9 0.035 >4 >35 >21 119 279 45.7 >21 35.3 307 0.038 >12 28.3 209 11.1 58.5 10.6 0.044 >10 >10 >10 >10
>104 3.2
O O O O O NH NH NH NH NH NH NH NH NH NH NH NH NH NH S S S S
J.2 J.2 K L L L M M M M N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1 N.1
0.47 0.3 0.2 0.09 3.2 0.7 19.8 >4 89.3 >21 4.3 6 1.7 5.3 1.4 1.1 0.21 3.4 1 0.87 2.6 11.6 0.81 0.15 >10 >10 >10 >10
>104 8.5 >2.6 >1.2 3700 6.1 1.4 2.2 0.35 9.5 1.3 0.43 >37.0 35.2 >21 116 63 156 70 14.4 59.3 0.044 >12 3 8.2 16.7 5.3 3 0.06 >10 >10 >10 >10
3 2 3 3 3 2 2 1 2 2 2 1 3 2 3 1 2 1 2 1 1 1 3 2 1 1 1 2 2 3 3 3 3
-CH2NH-
S
N.1
>10
>10
>10
3
-CH2-CH2S-CH2NH-CH2O-CH2NH-CH2NH-
NH O O O O O
N.1 N.1 N.1 N.1 N.1 N.1
>189 >26 13.5 14 >12 8.1
>130 >26 37 >42 >12 32.4
270 252 12 60.3 >12 16.2
2 3 1 2 3 1
OMe
30-4
OMe
N
OMe
18-3 10-18b 10-18c 23-7 23-8b 23-8 28-12 32-8 32-9 32-10 32-11 33-1 33-2 33-3 33-5 33-6 34-2 34-3 34-4 34-5 34-6 34-7 34-9 35-2 35-3 35-4 35-5 35-6 35-7 35-10 36-7a 36-7b 36-7c 36-7d 36-7e 37-1e 38-3 38-6 38-8 38-9 38-10
N
-CH2OH -CH2OH -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -3,4,5-OMe -2,5-OMe -3,4,5-OMe -2-Br,-3,4,5-OMe -3,4,5-OMe -4-L-Glu -4-L-Glu -3,4,5-OMe -3,4-Cl -2,5-OMe -3,4-OMe -4-OMe -2,5-OMe -2,5-OEt -3,4-Cl -2,3-(CH)4-4-L-Glu -2,5-OMe -3,4-Cl -2,3-(CH)4-3,4-OMe -3,4-Cl -2,3-(CH)4-4-L-Glu -3,4,5-OMe -2,5-OMe -3,4,5-OMe -2,5-OMe -3,5-Cl,-4-(1pyrrolo) -H -H -2,3-(CH)4-3,4-(CH)4-2-O-Ph -4-O-Ph
-Me -Me -Me -H
S 30 38-11 38-12 38-13 38-14 38-16 38-17 40-3 40-4
-2-Ph -3,4-(CH)4-2,5-Cl -3,4-Cl -3-OMe -2,5-OMe -Me -Me
40-5
-Me
40-6
-Me
40-7
-Me
40-8
-Me
40-table2-1 40-table2-2 40-table2-3 40-table-2-4 40-table-2-5 40-table-2-6
-CH2CH2C6H3-2,5OMe -Me -Me -Me -C6H4-4-Cl -CH2Ph -(CH2)4-
16-8a
-Me
40-9
16-12 16-10 36-6a 36-6b 36-6c 36-6d 36-6e 37-1a 37-1b 37-1c 37-1d 41-4c 41-4d 41-4e 41-4f 41-4g 41-4h 41-4i 41-5a
-CH2CH2C6H1-2-Br3,4,5-OMe -CH2NHC6H1-2-Br3,4,5-OMe -CH2NHC6H2-3,4,5OMe -CH2NHC6H3-2,5OMe -CH2N(Me)C6H23,4,5-OMe -CH2N(Me)C6H32,5-OMe -CH2NC6H3-3,5-Cl,4-(1-pyrrolo) -Ph -C6H4-4-Cl -C6H3-3,4-Cl -C6H2-3,4,5-OMe -CH2NH-1-fluorene -CH2NH-2-fluorene -CH2NH-3-(2methoxydibenzofuran) -CH2NH-3-(N-ethylcarbazole) -CH2NH-2-(9hydroxy-fluorene) -CH2NH-2-(9oxofluorene) -CH2NH-4-(9oxofluorene) -CH2N(Me)-3-(2methoxy-
-CH2NH-CH2N(Me)-CH2NH-CH2(Me)-CH2NH-CH2(Me)-C6H3-2,5-OMe -CH2C6H3-2,5-OMe -(CH2)2C6H3-2,5OMe -C6H2-3,4,5-OMe -CH2C6H2-3,4,5OMe -(CH2)2C6H2-3,4,5OMe
O O O O O O S S
N.1 N.1 N.1 N.1 N.1 N.1 N.2 N.2
7.7 14.8 50.9 44.8 >31.3 >27 4.8 14
45.4 23.6 >47 >27 >31.3 >27 0.13 0.07
137 14.6 71.9 >27 >31.3 >27 0.37 0.4
1 1 1 3 3 3 2 1
S
N.2
1.2
3.3
5.9
2
S
N.2
>8
0.32
1.8
2
S
N.2
>8
0.63
51
2
S
N.2
>8
18
25
2
-H
S
N.2
28
5.8
3.1
1
-Ph -C6H3-3,4-Cl -CH2Ph -Me -Me R1 -CH2C6H1-2-Br,3,4,5-OMe
S S S S S S
N.2 N.2 N.2 N.2 N.2 N.2
26 16 35 >100 >100 2.1
3.9 >28 6.2 >70 >100 2.8
57 4.6 14 >100 >37 3.9
1 2 1 3 3 2
S
N.2
>12
0.21
0.93
2
-H
S
N.2
49
2.5
2.8
1
-H
S
N.2
200
25
43
1
-Br
S
N.2
13
34
17
1
-Br
S
N.2
>100
>100
33
2
-Br
S
N.2
31
127
28
2
-Br
S
N.2
>10
>10
>10
3
-Br
S
N.2
7.5
26
10
2
-H -H -H -H -H -H
NH NH NH NH O O
N.2 N.2 N.2 N.2 N.2 N.2
>186 >161 33 8.3 >29 36.2
12 113 16 14 >29 27.7
9.1 62 23 27 >29 500
2 2 2 2 3 1
-H
O
N.2
10.3
>32
>32
3
-H
O
N.2
16.2
4.5
12.6
2
-H
O
N.2
>13
63
>13
3
-H
O
N.2
>63
>63
>63
3
-H
O
N.2
19.3
>38
>38
3
-H
O
N.2
>54
392
241
3
S 31
41-5b 41-7a 41-7b 41-7c 42-8 42-9 42-10 42-11 43-7 43-8 43-9 43-10 43-11 43-13 43-14 43-15 43-16 43-17 44-2 44-3 44-6 44-7 44-8 44-9 44-10 44-11 44-12 44-14 44-16 44-17 44-18 44-19 44-20 44-21 44-22 44-23 a
dibenzofuran) -CH2N(Me)-3-(Nethyl-carbazole) -CH2S-2-biphenyl -CH2S-3-biphenyl -CH2S-4-biphenyl -4-Cl -3,4-Cl -4-NO2 -3,4-OMe -2,5-OMe -3,5-OMe -2,4-OMe -3,4,5-OMe -2,5-Cl -2,4-Cl -3-Cl -2,5-OMe -3,5-OMe -3,4,5-OMe -Ph -C6H2-3,-4,5-OMe -C6H2-2,-4,5-OMe -C6H3-2,-5-OMe -C6H3-3,-5-OMe -C6H3-3,-4-OMe -C6H3-2,-4-OMe -C6H3-3,-4-Cl -C6H3-2,-6-Cl -C6H2-2-NO2-4,5OMe -4-pyridine -2-naphthyl -1-naphthyl-4-OMe -9-fluorenyl -CH2-Ph -CH2NH-C6H23,4,5-OMe -CH2NH-C6H3-2,5OMe -CH2S-2-naphthyl
-H
O
N.2
18.7
22.6
24.7
1
-H -H -H -S-S-S-S-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2NH-CH2N(Me)-CH2N(Me)-CH2N(Me)-
O O O
N.2 N.2 N.2 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 N.3 O O O O O O O O O
46 22 41 40 >20 >15 >21 47 20 16 22 25 15 26 56 87 45 153 59.4 22 37.4 9 12 14 19.5 11
105 23 79 3.1 11.7 244 20 2.2 2.6 7.1 9.3 0.66 2.2 3.5 10.3 4.2 37 28 2.2 1.5 1.7 3 14.2 2.4 6.7 11
49 31 351 24.6 >20 7470 >21 47 20 16 22 25 15 26 56 87 45 59.9 13 7 3.5 32.4 52.3 0.9 252 11
2 1 1 2 3 3 3 1 1 1 1 1 2 1 2 1 1 1 1 1 2 1 1 1 2 1
O
25
16.8
25
2
O O O O O
18 113 13 35 9.8
20 27 13 30.5 0.5
18 280 13 29.8 1.6
2 1 2 2 2
O
34
34
34
2
O
29
49
29
1
O
105
1.02
107
2
names are formed by hyphenating the reference number and the label given to the compound in the reference b IC50 values in µM for P. carinii (PC), T. gondii (TG) and rat liver (RL). Only RL activities are used in this work. c training set, test set and inactive compounds are indicated as 1, 2 and 3, respectively.
DHFR references* (1) Broughton, M. C.; Queener, S. F. Pneumocystis-carinii dihydrofolate-reductase used to screen potential antiPneumocystis drugs. Antimicrob. Agents Chemother. 1991, 35, 1348-1355. (6) Rosowsky, A.; Hynes, J. B.; Queener, S. F. Structure-activity and structure-selectivity studies on diaminoquinazolines and other inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolatereductase. Antimicrob. Agents Chemother. 1995, 39, 79-86.
S 32 (7) Gangjee, A.; Elzein, E.; Queener, S. F.; McGuire, J. J. Synthesis and biological activities of tricyclic conformationally restricted tetrahydropyrido annulated furo[2,3-d] pyrimidines as inhibitors of dihydrofolate reductases. J. Med. Chem. 1998, 41, 1409-1416. (8) Gangjee, A.; Adair, O.; Queener, S. F. Synthesis of 2,4-diamino-6-(thioarylmethyl)pyrido [2,3- d]pyrimidines as dihydrofolate reductase inhibitors. Bioorg. Med. Chem. 2001, 9, 2929-2935. (9) Piper, J. R.; Johnson, C. A.; Krauth, C. A.; Carter, R. L.; Hosmer, C. A. et al. Lipophilic antifolates as agents against opportunistic infections .1. Agents superior to trimetrexate and piritrexim against Toxoplasma gondii and Pneumocystis carinii in in vitro evaluations. J. Med. Chem. 1996, 39, 1271-1280. (10) Graffner-Nordberg, M.; Kolmodin, K.; Aqvist, J.; Queener, S. F.; Hallberg, A. Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. J. Med. Chem. 2001, 44, 2391-2402. (11) Jackson, H. C.; Biggadike, K.; McKilligin, E.; Kinsman, O. S.; Queener, S. F. et al. 6,7-disubstituted 2,4diaminopteridines: Novel inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase. Antimicrob. Agents Chemother. 1996, 40, 1371-1375. (12) Rosowsky, A.; Cody, V.; Galitsky, N.; Fu, H. N.; Papoulis, A. T. et al. Structure-based design of selective inhibitors of dihydrofolate reductase: Synthesis and antiparasitic activity of 2,4- diaminopteridine analogues with a bridged diarylamine side chain. J. Med. Chem. 1999, 42, 4853-4860. (13) Rosowsky, A.; Mota, C. E.; Wright, J. E.; Queener, S. F. 2,4-diamino-5-chloroquinazoline analogs of trimetrexate and piritrexim - synthesis and antifolate activity. J. Med. Chem. 1994, 37, 4522-4528. (14) Rosowsky, A.; Forsch, R. A.; Queener, S. F. 2,4-diaminopyrido[3,2-d]pyrimidine inhibitors of dihydrofolatereductase from Pneumocystis carinii and Toxoplasma gondii. J. Med. Chem. 1995, 38, 2615-2620. (15) Gangjee, A.; Vidwans, A. P.; Vasudevan, A.; Queener, S. F.; Kisliuk, R. L. et al. Structure-based design and synthesis of lipophilic 2,4-diamino-6-substituted quinazolines and their evaluation as inhibitors of dihydrofolate reductases and potential antitumor agents. J. Med. Chem. 1998, 41, 3426-3434. (16) Rosowsky, A.; Mota, C. E.; Queener, S. F. Brominated trimetrexate analogues as inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase. J. Heterocycl. Chem. 1996, 33, 1959-1966. (18) Rosowsky, A.; Fu, H. N.; Queener, S. F. Synthesis of 2,4-diaminopyrido[2,3-d]pyrimidines and 2,4diaminoquinazolines with bulky dibenz[b,f]azepine and dibenzo[a,d]-cycloheptene substituents at the 6-position as inhibitors of dihydrofolate reductases from Pneumocystis carinii, Toxoplasma gondii, and Mycobacterium avium. J. Heterocycl. Chem. 2000, 37, 921-926. (19) Gangjee, A.; Zaveri, N.; Kothare, M.; Queener, S. F. Nonclassical 2,4-diamino-6-(aminomethyl)-5,6,7,8tetrahydroquinazoline antifolates - synthesis and biological- activities. J. Med. Chem. 1995, 38, 3660-3668. (20) Rosowsky, A.; Papoulis, A. T.; Forsch, R. A.; Queener, S. F. Synthesis and antiparasitic and antitumor activity of 2,4- diamino-6-(arylmethyl)-5,6,7,8-tetrahydroquinazoline analogues of piritrexim. J. Med. Chem. 1999, 42, 1007-1017. (21) Gangjee, A.; Zhu, Y. M.; Queener, S. F.; Francom, P.; Broom, A. D. Nonclassical 2,4-diamino-8-deazafolate analogues as inhibitors of dihydrofolate reductases from rat liver, Pneumocystis carinii, and Toxoplasma gondii. J. Med. Chem. 1996, 39, 1836-1845. (22) Gangjee, A.; Zhu, Y. M.; Queener, S. F. 6-substituted 2,4-diaminopyrido[3,2-d]pyrimidine analogues of piritrexim as inhibitors of dihydrofolate reductase from rat liver, Pneumocystis carinii, and Toxoplasma gondii and as antitumor agents. J. Med. Chem. 1998, 41, 4533-4541. (23) Gangjee, A.; Shi, J. F.; Queener, S. F.; Barrows, L. R.; Kisliuk, R. L. Synthesis of 5-methyl-5-deaza nonclassical antifolates as inhibitors of dihydrofolate reductases and as potential antipneumocystis, antitoxoplasma, and antitumor agents. J. Med. Chem. 1993, 36, 3437-3443. (24) Gangjee, A.; Vasudevan, A.; Queener, S. F.; Kisliuk, R. L. 6-substituted 2,4-diamino-5-methylpyrido[2,3d]pyrimidines as inhibitors of dihydrofolate reductases from Pneumocystis carinii and Toxoplasma gondii and as antitumor agents. J. Med. Chem. 1995, 38, 1778-1785. (25) Gangjee, A.; Vasudevan, A.; Queener, S. F.; Kisliuk, R. L. 2,4-diamino-5-deaza-6-substituted pyrido[2,3d]pyrimidine antifolates as potent and selective nonclassical inhibitors of dihydrofolate reductases. J. Med. Chem. 1996, 39, 1438-1446. (26) Gangjee, A.; Vasudevan, A.; Queener, S. F. Synthesis and biological evaluation of nonclassical 2,4- diamino-5methylpyrido[2,3-d]pyrimidines with novel side chain substituents as potential inhibitors of dihydrofolate reductases. J. Med. Chem. 1997, 40, 479-485. (27) Gangjee, A.; Adair, O.; Queener, S. F. Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase inhibitors and antitumor agents: Synthesis and biological activities of 2,4-diamino-5-methyl-6[(monosubstituted anilino)methyl]pyrido[2,3-d]pyrimidines. J. Med. Chem. 1999, 42, 2447-2455.
S 33 (28) Gangjee, A.; Devraj, R.; Queener, S. F. Synthesis and dihydrofolate reductase inhibitory activities of 2,4diamino-5-deaza and 2,4-diamino-5,10-dideaza lipophilic antifolates. J. Med. Chem. 1997, 40, 470-478. (29) Rosowsky, A.; Forsch, R. A.; Queener, S. F. Inhibition of Pneumocystis carinii, Toxoplasma gondii, and Mycobacterium avium dihydrofolate reductases by 2,4-diamino-5-[2-methoxy-5-[omegacarboxyalkyloxy)benzyl]pyrimidines: Marked improvement in potency relative to trimethoprim and species selectivity relative to piritrexim. J. Med. Chem. 2002, 45, 233-241. (30) Gangjee, A.; Vasudevan, A.; Queener, S. F. Bicylic conformationally restricted analogs of nonclassical pyrido[2,3-d] pyrimidines as potential inhibitors of dihydrofolate reductases. Chemistry and biology of pteridines and folates; Plenum Press: New York, 1993; pp 449-453. (31) Gangjee, A.; Zeng, Y. B.; McGuire, J. J.; Kisliuk, R. L. Synthesis of classical and nonclassical, partially restricted, linear, tricyclic 5-deaza antifolates. J. Med. Chem. 2002, 45, 5173-5181. (32) Rosowsky, A.; Mota, C. E.; Queener, S. F. Synthesis and antifolate activity of 2,4-diamino-5,6,7,8tetrahydropyrido[4,3-d]pyrimidine analogs of trimetrexate and piritrexim. J. Heterocycl. Chem. 1995, 32, 335340. (33) Gangjee, A.; Devraj, R.; McGuire, J. J.; Kisliuk, R. L.; Queener, S. F. et al. Classical and nonclassical furo[2,3d]pyrimidines as novel antifolates - synthesis and biological-activities. J. Med. Chem. 1994, 37, 1169-1176. (34) Gangjee, A.; Mavandadi, F.; Queener, S. F.; McGuire, J. J. Novel 2,4-diamino-5-substituted-pyrrolo[2,3d]pyrimidines as classical and nonclassical antifolate inhibitors of dihydrofolate reductases. J. Med. Chem. 1995, 38, 2158-2165. (35) Gangjee, A.; Mavandadi, F.; Queener, S. F. Effect of n-9-methylation and bridge atom variation on the activity of 5-substituted 2,4-diaminopyrrolo[2,3-d]pyrimidines against dihydrofolate reductases from Pneumocystis carinii and Toxoplasma gondii. J. Med. Chem. 1997, 40, 1173-1177. (36) Rosowsky, A.; Papoulis, A. T.; Queener, S. F. 2,4-diaminothieno [2,3-d]pyrimidine lipophilic antifolates as inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase. J. Med. Chem. 1997, 40, 3694-3699. (37) Rosowsky, A.; Fu, H. N.; Queener, S. F. Synthesis of new 2,4-diamino-7h-pyrrolo[2,3-d]pyrimidines via the taylor ring transformation/ring annulation strategy. J. Heterocycl. Chem. 2001, 38, 1197-1202. (38) Gangjee, A.; Guo, X.; Queener, S. F.; Cody, V.; Galitsky, N. et al. Selective Pneumocystis carinii dihydrofolate reductase inhibitors: Design, synthesis, and biological evaluation of new 2,4-diamino-5-substituted-furo[2,3d]pyrimidines. J. Med. Chem. 1998, 41, 1263-1271. (39) Gangjee, A.; Yu, J. M.; McGuire, J. J.; Cody, V.; Galitsky, N. et al. Design, synthesis, and X-ray crystal structure of a potent dual inhibitor of thymidylate synthase and dihydrofolate reductase as an antitumor agent. J. Med. Chem. 2000, 43, 3837-3851. (40) Rosowsky, A.; Mota, C. E.; Wright, J. E.; Freisheim, J. H.; Heusner, J. J. et al. 2,4-diaminothieno[2,3d]pyrimidine analogs of trimetrexate and piritrexim as potential inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate-reductase. J. Med. Chem. 1993, 36, 3103-3112. (41) Gangjee, A.; Dubash, N. P.; Queener, S. F. The synthesis of new 2,4-diaminofuro[2,3-d]pyrimidines with 5biphenyl, phenoxyphenyl and tricyclic substitutions as dihydrofolate reductase inhibitors. J. Heterocycl. Chem. 2000, 37, 935-942. (42) Gangjee, A.; Mavandadi, F.; Kisliuk, R. L.; McGuire, J. J.; Queener, S. F. 2-amino-4-oxo-5-substitutedpyrrolo[2,3-d]pyrimidines as nonclassical antifolate inhibitors of thymidylate synthase. J. Med. Chem. 1996, 39, 4563-4568. (43) Gangjee, A.; Vidwans, A.; Elzein, E.; McGuire, J. J.; Queener, S. F. et al. Synthesis, antifolate, and antitumor activities of classical and nonclassical 2-amino-4-oxo-5-substituted-pyrrolo[2,3- d]pyrimidines. J. Med. Chem. 2001, 44, 1993-2003. (44) Gangjee, A.; Vasudevan, A.; Queener, S. F. Conformationally restricted analogues of trimethoprim: 2,6diamino-8-substituted purines as potential dihydrofolate reductase inhibitors from Pneumocystis carinii and Toxoplasma gondii. J. Med. Chem. 1997, 40, 3032-3039. (45) Rosowsky, A.; Papoulis, A. T.; Queener, S. F. 2,4-diamino-6,7-dihydro-5h-cyclopenta[d]pyrimidine analogues of trimethoprim as inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase. J. Med. Chem. 1998, 41, 913-918. (46) Then, R. L.; Hartman, P. G.; Kompis, I.; Santi, D. Selective inhibition of dihydrofolate reductase from problem human pathogens. Chemistry and biology of pteridines and folates; Plenum Press: New York, 1993; pp 533536. (47) Gangjee, A.; Shi, J. F.; Queener, S. F. Synthesis and biological activities of conformationally restricted, tricyclic nonclassical antifolates as inhibitors of dihydrofolate reductases. J. Med. Chem. 1997, 40, 1930-1936.
S 34 (48) Gangjee, A.; Mavandadi, F.; Queener, S. F. Synthesis and biological activity of tricyclic, conformationally restricted analogs of lipophilic pyrido[2,3-d]-pyrimidine antifolates. Chemistry and biology of pteridines and folates; Plenum Press: New York, 1993; pp 441-449. (49) Gangjee, A.; Mavandadi, F.; Queener, S. F. Conformationally restricted tricyclic analogues of lipophilic pyrido[2,3-d]pyrimidine antifolates. J. Heterocycl. Chem. 2001, 38, 213-220. (50) Rosowsky, A.; Papoulis, A. T.; Queener, S. E. One-step synthesis of novel 2,4-diaminopyrimidine antifolates from bridged alicyclic ketones and cyanoguanidine. J. Heterocycl. Chem. 1999, 36, 723-728. (51) Donkor, I. O.; Devraj, R.; Queener, S. F.; Barrows, L. R.; Gangjee, A. Synthesis of a series of diaminobenzo[f]and diaminobenzo[h]pyrimido[4,5-b]quinolines as 5-deaza tetracyclic nonclassical antifolates. J. Heterocycl. Chem. 1996, 33, 1653-1661. * Reference numbers are not sequential to keep them consistent with our previous classification work
GPB, THER, THR Table A.1.10. GPB inhibitor sets Training set 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 16, 18, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 41, 43, 44, 45, 49, 50, 51, 53, 56, 58, 59, 60, 61, 64 Test set 8, 12, 15, 17, 19, 22, 23, 29, 33, 40, 42, 46, 47, 48, 52, 54, 55, 57, 62, 63, 65, 66 Table A.1.11. THER inhibitor sets Training set ACE_OHLEU_AGNH2, BZSAG, C6PLTNME, CH3COCH2CO_FAGNH2, CLTZNCRYS, DAH51, DAH52, DAH53, NHOHBZMAGNH2, NHOHBZMAGOH, OHBZMAGNH2, ZALA, ZAPOLA, ZFGNH2, ZFPOLA, ZGGLNHOH, ZGG_D_LNHOH, ZGLNH2, ZGLNHOH, ZGLY, ZGPCLA, ZGPCLF, ZGPCLG, ZGPCLLZNCRYS, ZGPLA, ZGPLF, ZGPLG, ZGPLLZNCRYS, ZGPOLA, ZGPOLF, ZGPOLLZNCRYS, ZGPOLNH2, ZG_D_LNHOH, ZLGNH2, ZLPOLA, Z_D_APOLA, Z_D_FPLA, Z_D_FPOLA, Z_NH_GLNHOH, C6POLTNME, CHO_OHLEU_AGNH2, DAH50, NHOHMALAGNH2, PAAOH, PPHEOH, PPPHE, PO3_FAGNH2, P_OPHE_OME_LEUNH2, ZGLNMEOH, ZGPLNH2, ZGPOLG Test set C6PCLTNME, DAH55, HOCH2CO_FAGNH2, NHOHIBMAGNH2, PLFOH, PNHET, P_ILE_AOH, R_THIORPHAN, SO3_FAGNH2, ZFPLAZNCRYS, ZGPCLNH2, Z_D_LPOLA, CBZPHE, CH3O2S_FAGNH2, DAH54, NHOHBZMAGNA, NHOHBZMOET, NHOHLEU, PHOSPHORAMIDON, PLEUNH2, S02P_FAGNH2, S_THIORPHAN, ZGGNHOH, ZYGNH2, Z_NH_GLNH2
S 35
Table A.1.12. THR inhibitor sets Training set 2, 3, 4, 6, 8, 9, 12, 13, 15, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 45, 47, 48, 50, 52, 53, 55, 57, 59, 60, 62, 63, 64, 66, 68, 69, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 85, 86, 87, 88 Test set 1, 5, 7, 10, 11, 14, 16, 20, 21, 29, 30, 31, 35, 39, 44, 46, 49, 51, 54, 56, 58, 61, 65, 67, 70, 71, 72, 81, 82
A.2. Values of q2L20%O and q2L33%O, and thresholds for defining outliers Table A.2.1. Values of q2L20%O and q2L33%O, and thresholds used for defining q2LOO outliers for PLS analyses CoMFA
CoMSIA basic
CoMSIA extra
q2L20%O q2L33%O thresh
0.67 0.65 2.00
0.65 0.63 2.00
0.66 0.64 2.00
q2L20%O q2L33%O thresh
0.49 0.42 2.00
0.41 0.37 2.35
2
EVA
HQSAR
2D
2.5D
0.70 0.67 2.09
0.71 0.70 2.00
0.67 0.66 2.05
0.71 0.67 2.00
AchE 0.44 0.36 0.41 0.29 2.00 2.00
0.29 0.19 2.00
0.31 0.29 1.96
0.30 0.28 2.00
ACE
BZR
q L20%O q2L33%O thresh
0.31 0.28 2.00
0.38 0.37 2.18
0.44 0.41 2.00
0.39 0.38 2.00
0.38 0.36 2.00
0.36 0.33 2.06
0.33 0.30 2.00
q2L20%O q2L33%O thresh
0.46 0.43 2.00
0.38 0.39 2.00
COX2 0.55 0.43 0.55 0.40 2.02 2.00
0.47 0.45 2.00
0.47 0.43 1.97
0.51 0.49 2.00
q2L20%O q2L33%O thresh
0.63 0.62 2.00
0.62 0.61 2.00
DHFR 0.64 0.61 0.63 0.58 2.00 2.00
0.68 0.66 2.00
0.50 0.49 2.00
0.51 0.48 2.00
S 36 Table A.2.1. (continued) CoMFA
CoMSIA basic
CoMSIA extra
0.37 0.33 2.00
0.24 0.09 2.00
0.58 0.54 2.00
0.44 0.42 2.00
EVA
HQSAR
2D
2.5D
0.51 0.42 2.00
0.66 0.65 2.00
0.26 0.22 1.96
0.39 0.31 2.04
THER 0.46 0.41 0.43 0.35 2.00 2.00
0.44 0.41 2.00
0.57 0.51 2.00
0.60 0.56 2.00
0.40 0.28 2.08
0.55 0.50 1.98
0.43 0.38 2.00
GPB
q2L20%O q2L33%O thresh 2
q L20%O q2L33%O thresh
0.45 0.42 2.00
THR
2
q L20%O q2L33%O thresh
0.47 0.40 2.00
0.49 0.42 2.00
0.65 0.58 2.00
0.44 0.34 2.00
Table A.2.2. Thresholds for defining r2test outliers for PLS analyses CoMFA ACE AchE BZR COX2 DHFR GPB THER THR
2.00 2.00 2.00 2.06 2.00 2.00 2.00 2.00
CoMSIA basic 1.97 2.00 2.00 2.05 2.00 2.00 2.00 2.00
CoMSIA extra 2.00 2.00 1.90 2.00 1.98 2.00 2.00 2.00
EVA
HQSAR
2D
2.5D
2.00 2.00 2.00 2.00 1.97 2.05 1.92 2.00
1.97 2.08 2.00 2.00 2.05 2.05 2.00 2.00
1.96 2.00 2.00 1.95 1.95 2.00 2.00 2.00
2.05 2.00 2.03 2.05 2.01 2.00 2.00 2.00
Table A.2.3. Thresholds for defining r2test outliers for 2.5D descriptors with various modelbuilding methods
ACE AchE BZR COX2 DHFR GPB THER THR
PLS
GFA-l
2.05 2.00 2.03 2.05 2.01 2.00 2.00 1.80*
2.05 1.98 2.00 2.08 2.00 2.00 2.00 2.00
GFA-lens 2.00 2.00 2.00 2.00 2.01 2.00 2.02 2.08
GFAnl 1.92 2.00 2.00 2.00 2.00 2.00 2.02 2.00
GFAnl-ens 2.00 2.00 2.00 2.00 2.00 2.05 2.04 2.00
GPLS 2.00 2.00 2.00 2.05 2.01 2.00 2.00 2.00
GPLSens 1.98 2.00 2.00 1.99 2.06 2.00 2.00 2.00
NN 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.06
NNens 2.00 2.00 1.93 2.00 2.00 2.05 2.00 2.00
S 37 Table A.2.4. Test set outliers ACE
COO_24A
MOL_10
AchE
COX2
DHFR
GPB
CoMFA 1-351521 5-1H 22-20 RO15-2201 8-1V 22-21 1-31C RO16-4234 8-2C 57 29-2 RO15-8852 8-1AK 28-12 11-29 40-3
2-36
2-36
COO_24A THIOL_28
BZR
3-18
CoMSIA basic 9-12T 5-1H 22-21 RO15-2201 8-22F 29-2 RO16-4234 8-8A 32-11 RO15-8852 8-20E 40-7 8-1AK 40-8 CoMSIA extra 9-12T 5-1H 22-21 RO15-2201 8-8A 29-2 RO16-4234 8-20E 24-3E RO15-8852 12-10B 36-6C 40-7 EVA 25-26 8-22F 24-3E RO15-2201 8-2C 36-6C RO16-4234 8-8A 36-6E RO15-8852 8-22C 44-16 8-23 40-8
THER
THR
CH3O2S_FAGNH2 71
57
CH3O2S_FAGNH2 71
57
DAH55 71 CH3O2S_FAGNH2
57
67
HQSAR 1-137545 5-1H 1-184692 8-1V 22-21 MOL_32 2-36 RO16-4234 57 8-8A 29-2 SQ29852_2P 3-12A RO15-8852 8-20E 24-3E 8-22C 28-12
7 CH3O2S_FAGNH2 58 67
S 38
ACE
MOL_10
AchE
BZR
COX2
DHFR
GPB
2D 1-351521 8-22F 22-21 RO15-2201 8-8A 29-2 3-13A RO16-4234 8-20E 24-3E RO15-8852 8-22C 40-T-2-6 8-23
MOL_10 1-3O SQ29852_2P 2-36
2.5D-GFA-l-ens 6-2 5-1H 22-21 8-1V 29-2 RO14-3074 8-8A 36-6C RO21-8482 8-20E 44-20 8-22C 28-6
SQ29852_2P THIOL_28
MOL_10
2-32 2-36
THR
CH3O2S_FAGNH2 10
2.5D 1-351521 3-33 22-21 RO14-3074 5-1H COO_24A 2-32 29-2 RO16-4234 7-20P 24-3E SQ29852_2P 3-13A RO15-8852 8-22E 28-6 8-8A 34-5 2.5D-GFA-l 6-2 1-31 6-13 3-33 RO14-3074 5-1H 22-21 RO21-8482 8-22E 29-2 RO16-4234 8-1V 44-20 8-8A 28-6
THER
CH3O2S_FAGNH2
10 67
57
DAH55
10 67
57
CH3O2S_FAGNH2
10 67
2.5D-GFA-nl 6-48 5-1H 1-351521 22-21 RO14-3074 8-2F 57 RO22-1274 8-8A 29-2 RO16-4234 8-20E 24-3E 8-22C 37-1E 34-5
10 CH3O2S_FAGNH2 67 71
S 39
ACE
AchE
COO_24A 2-32 THIOL_28 2-36
COO_23E COO_24A
COO_24A MOL_10
THIOL_28 2-36
MOL_10 2-32 THIOL_28 2-36
BZR
COX2
DHFR
GPB
2.5D-GFA-nl-ens 1-351521 5-1H 22-21 RO14-3074 8-2F 29-2 RO22-1274 8-8A 65 24-3E RO16-4234 8-20E 28-6 8-22C 34-5
RO14-3074 RO15-2201 RO16-4234 RO15-8852
RO14-3074 RO15-2201 RO16-4234 RO15-8852
2.5D-GPLS 1-351521 3-33 22-21 5-1H 29-2 7-20P 24-3E 8-22E 28-6 8-20E 34-5 2.5D-GPLS-ens 1-351521 3-33 22-21 5-1H 29-2 7-20P 24-3E 8-22E 36-6C 8-20E 28-6
2.5D-NN 6-13 5-1H 22-21 7-20P 24-3E RO16-4234 8-1V 40-T-2-6 RO15-8852 8-8A 28-6 8-22C 40-7
57
2.5D-NN-ens 1-152737 5-1H 6-2 RO14-3074 7-20P 6-13 57 RO16-4234 8-1V 22-21 RO15-8852 8-8A 24-3E 8-22C 28-6
THER
THR
10 CH3O2S_FAGNH2 67 71
CH3O2S_FAGNH2
10 67
CH3O2S_FAGNH2
10 67
DAH55
10 71
DAH55
10 67
S 40 A.3. Alignment procedures for CoMFA, CoMSIA ACE: The alignment is described in ref. 1 [reference list below]. AchE: We use the 3 pharmacophore features described by Golbraikh et al.2 (i.e. the benzyl group, the positively charged nitrogen atom of the piperidine group and the carbonyl acceptor in E2020) for aligning compounds. The conformation of E2020 was determined using the MCMM routine in Macromodel 7.2 (Schrodinger; Portland, OR) with the MMFF94S force field and GBSA implicit solvation model (500 Monte Carlo steps, other parameters default), and rigidly superposed on E2020 complexed with AchE (PDB 1eve). The lowest-energy conformation has a heavy-atom root-mean-square deviation (RMSD) of 0.9 Å when compared to the conformation extracted from the crystal structure. We did not use the ligand-bound conformation deduced from the crystal structure, as the purpose of a project using this set was to develop receptor surface models useful in the absence of such information. The same holds for the COX2 set. Other compounds were minimised with MMFF94S in GBSA implicit solvent and flexibly fit onto E2020 using the alignment module in Cerius2 (i.e. allowing rotation of free torsions). BZR: All ligands have been aligned onto diazepam, which was subjected to the same MCMM optimisation described for the AchE inhibitor E2020. As discussed in ref. 3, there are two lowenergy ring conformations for diazepam. Ring conformation “a” in Figure 10 of the above reference was used, as it is the bioactive conformation. Other compounds were minimised with MMFF94S in GBSA implicit solvent and flexibly fit onto diazepam using the shared fused ring system and phenyl group. Substituents were placed in a consistent fashion. Substituents on the rotatable phenyl ring of diazepam were placed on the edge nearest the fused ring structure (i.e. the "left" edge when depicted in the orientation given for BZR family A.1 in Table A.1.4), as that orientation has a lower energy compared to the alternate orientation having the phenyl ring rotated by 180° about its torsion. We use the syn conformation for esters such as Ro14-5974 (as depicted in Figure 1) instead of the anti conformation suggested by Cook et al.4,5 The syn conformer gives better overlap with other classes of BZR ligands, and has a B3LYP/6311+G(d,p) // HF/6-31G* energy only 2.1 kcal/mol higher than that of the anti conformer. COX2: The MCMM procedure discussed for the AchE inhibitor E2020 was applied to 8celecoxib. 8-celecoxib was superposed on the inhibitor SC558 in the PDB structure 1CX2. Note however that the inhibitors were not docked into the protein, but merely placed in the active site. In particular, the phenyl-SO2-X torsion determined by conformational searching is not the same as that in the crystal structure 1CX2. The other inhibitors were minimised with MMFF94S in GBSA implicit solvent and flexibly superposed on 8-celecoxib using three atoms on each of the three rings. Substituents were placed in a consistent fashion. For example, substituents R2 on the second vicinal ring (referring to the COX2 family A.1 in Table A.1.6) were always placed away from the first vicinal ring. The energy difference is very small between that orientation, and another in which the phenyl ring has been rotated by 180° about its torsion. As such, if one were to have no protein structure to aid in the alignment, it is best to be consistent as opposed to always choosing the global energy minimum.
S 41 DHFR: The crystal structures for several ligand - P. carinii (pc) DHFR complexes have been used for aligning compounds. The pcDHFR-bound structures of 33-2 (PDB 1daj) and 12-4b (PDB 1klk) were rigidly superposed onto folate (PDB 1cd2) using the atom mappings implied by folate labels shown in Figure A.1; the root-mean-square deviations (RMSDs) with respect to folate are 0.3 Å for 33-2 and 0.4 Å for 12-4b when calculated with the atoms used for the superposition. All other compounds were flexibly fit onto the most similar of these three templates. With the positions of the pyridine (having un-primed numbers in Figure A.1) and phenyl rings (having primed numbers in Figure A.1) fixed, structures were relaxed using the CFF97 force field in Cerius2 with no cut-off for van der Waals or electrostatic interactions (other parameters default). Substituents on the phenyl ring were placed in a consistent fashion, with preference for the solvent-exposed edge of the phenyl ring: the 2’ position was occupied before 6’ and the 3’ position before 5’, with the ortho position taking precedence over the meta position when both are substituted. This placement of substituents is consistent with that observed for the methoxy groups in 15-11 (PDB 1ly3) and the dibenzo[b,f]azepine ring in 12-4b. The active site geometry of pc and human (for which rat liver is a surrogate) enzymes is very similar, and the heavy-atom RMSDs for several inhibitors complexed to pc and human DHFR following rigid superposition are small (15-11: 1ly3 vs. 1boz, 0.4 Å; folate: 1cd2 vs 1drf, 0.7 Å; 33-2: 1daj vs. 1hfp, 0.6 Å; the latter two are reduced by half if the solvent-exposed glutamate side chain is excluded).
Figure A.1. DHFR inhibitors. Numbers for MTX, TMQ, PTX, 33-2, 12-4b show mapping of atoms to folate used for aligning compounds. GPB, THERM, THR: Alignment procedures for GPB and THERM are described in reference 6. The alignment procedure for THR is described in reference 7.
S 42
References (1) Depriest, S. A.; Mayer, D.; Naylor, C. B.; Marshall, G. R. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors - a comparison of CoMFA models based on deduced and experimentally determined active-site geometries. J. Am. Chem. Soc. 1993, 115, 5372-5384. (2) Golbraikh, A.; Bernard, P.; Chretien, J. R. Validation of protein-based alignment in 3D quantitative structureactivity relationships with CoMFA models. Eur. J. Med. Chem. 2000, 35, 123-136. (3) Haefely, W.; Kyburz, E.; Gerecke, M.; Mohler, H. Recent advances in the molecular pharmacology of benzodiazepine receptors and in the structure-activity relationships of their agonists and antagonists. Adv. Drug Res. 1985, 14, 165-322. (4) Zhang, W.; Koehler, K. F.; Zhang, P.; Cook, J. M. Development of a comprehensive pharmacophore model for the benzodiazepine receptor. Drug Des. Discov. 1995, 12, 193-248. (5) Huang, Q.; He, X. H.; Ma, C. R.; Liu, R. Y.; Yu, S. et al. Pharmacophore/receptor models for GABA(A)/BZR subtypes (alpha 1 beta 3 gamma 2, alpha 5 beta 3 gamma 2, and alpha 6 beta 3 gamma 2) via a comprehensive ligand-mapping approach. J. Med. Chem. 2000, 43, 71-95. (6) Gohlke, H.; Klebe, G. Drugscore meets CoMFA: Adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J. Med. Chem. 2002, 45, 4153-4170. (7) Bohm, M.; Sturzebecher, J.; Klebe, G. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa. J. Med. Chem. 1999, 42, 458477.
A.4. Description of grids used for CoMFA, CoMSIA ACE AchE BZR COX2 DHFR x min -12 -12 -12 12 4 x max 16 12 14 38 26 y min -16 50 -10 14 -4 y max 12 76 12 32 18 z min -10 54 -10 4 -4 z max 12 82 12 28 22 all grids use 2 Å step size, C.3 probe atom with charge +1
GPB THERM -12 -10 12 16 -8 -18 10 12 -8 -12 14 10
THR -6 20 -18 4 -2 24
S 43 A.5. 2.5D descriptors used as inputs for neural network models ACE: SdO, chi-0, JX, FH20, FPSA-2, DPSA-1, shadow-YZfrac AchE: SddsN, JX, dipole-mag, RPSA, shadow-XZfrac BZR: SsssN, kappa-3, radius-of-gyration, FPSA-1, FPSA-3, PPSA-3, WPSA-3, RPSA COX2: SdO, SaaN, SC-2, RNCG, RPCG DHFR: SaaaC, SaasC, chi-v-1, chi-v-3_p, MW, MolRef, PPSA-1, PPSA-2, FPSA-3, TASA GPB: SssNH, kappa-2, shadow-Xyfrac THR: SsssCH, NaasC, NsssCH, Hbond_acceptors, chi-v-2, FH2O, PMI-mag, WPSA-3 THERM: SssO, IC, Rotlbonds, AlogP98, PPSA-1 A.6. Notes on electronic files Files in MDL SD and Sybyl mol2 formats are provided. The files are tarred and gzipped contents of the directories listed below (see UNIX commands tar and gzip), stored within a Windows WinZip archive (only ZIP is supported by the ACS; use unzip for opening under Linux). When .tar.gz files are opened in WinZip, the directory structure is not visible; use “extract …” in the action menu rather than drag-and-drop for preserving the directory structure. 3dqsar_mol2: Sybyl mol2 databases of aligned compounds, and tab-separated text files containing spreadsheet data. 3dqsar_sd: MDL SD files of aligned compounds (the format does not allow specification of charges; use the mol2 databases if you want our calculated charges). corina_sd: MDL SD files of CORINA-generated structures. 25d_descriptors: contains tab-separated 2.5D descriptors for each set. File contents: • Min_dist indicates the Tanimoto coefficient calculated between each test set compound and the most similar training set compound; Avg_dist is the average value calculated over all training set compounds. These may be viewed as measures for the degree of extrapolation from the training set. • In the set column, 1, 2 and 3 indicate training, test and inactive compounds, respectively. • In the SD file of CORINA structures for the DHFR set, activities in µM are given for P. carinii (PC) and T. gondii (TG) in addition to rat liver (RL); only RL activities are used in this work.
