Supporting information IDENTIFICATION OF NOVEL SEROTONIN TRANSPORTER COMPOUNDS BY VIRTUAL SCREENING
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1 upporting information IDETIICATI VEL ERTI TRAPRTER CMPUD BY VIRTUAL CREEIG Mari Gabrielsen, Rafał Kurczab, Agata iwek, Małgorzata Wolak, Aina W. Ravna,Kurt Kristiansen,Irina Kufareva, Ruben Abagyan, Gabriel owak, Zdzisław Chilmonczyk, Ingebrigt ylte and Andrzej J. Bojarski igure 1. Additional 3D ligand-based pharmacophore models igure 2. pectral data igure 3. Radioligand binding curves Table 1. Reference ligands Table 2. Metrics-threshold optimisation details Table 3. ummary, in vitro screening Table 4. ummary, in vitro full binding assays Pages 2 3 Pages 4 6 Pages 7 9 Pages Page 13 Pages Pages
2 igure 1. 3D ligand-based pharmacophore models. ne reference ligand from each class is mapped. Blue sphere: hydrophobic feature; range sphere: aromatic feature; Red sphere: positive ionisable feature; Green sphere: hydrogen bond acceptor feature; Magenta sphere: hydrogen bond donor feature. RI/RI TCA Mazindol 3-Phenyltropane Radioligand luvoxamine 2
3 ()-Citalopram ertraline luoxetine/venlafaxine 3
4 igure 2. pectral data for the most active representative of clusters C01 C16 as supported by vendors (Asinex, ChemBridge, ChemDiv, Enamine, Life Chemicals) see Table 3. C01 A C02 T R K R Dovbiy C PPM PPM ile name: R Date: 07-ov perator:reutova olvent: : Mz W: 7199 z C: 0 TE: 303 K PW: 7.50 usec, RG: 48 AQ: 2.00 sec, RD: 0.00 sec I: *R317282* C C04 T C C
5 C C08 BA C09 C C10 T C11 T C12 T C PPM 2.06 PPM ile name: Klishin : Mz C: 0 PW: 7.50 usec, RG: 30 I: Date: 02-ov-2009 olvent: DM-d6 + C4 W: 6803 z TE: 293 K AQ: 1.33 sec, RD: 0.00 sec 5
6 C13 E C R K R Dovbiy C PPM PPM ile name: R Date: 20-Dec perator:reutova olvent: : Mz W: 6398 z C: 0 TE: 293 K PW: 7.00 usec, RG: 38 AQ: 1.80 sec, RD: 0.00 sec I: *R320942* C C16 BA PPM PPM f PPM 3 C PPM K(0) ile name: f Expert: A.Ryabitsky : Mz; sw: 8000 z; at: 1.50 sec : ; pw: 9,65 usec I: 65536, TD: Date: 04_oct_2013 olvent: DM 0928 TE: 293 K block: s
7 igure 3. Radioligand binding curves. Concentration-dependent inhibition of specific [ 3 ]-citalopram binding to ERT in rat neocortical tissue by the highest affinity representative of clusters C1 C16 (see Table 3) and for three reference compounds: Imipramine, Citalopram and luoxetine. Data are from the mean of two independent experiments. C01 A C02 T C C04 T C C
8 C C08 BA C09 C C10 T C11 T C12 T C13 E C
9 C C16 BA Imipramine, K i = 28.1 nm (EM ± 1.4) a Escitalopram, K i = 1.1 nm (EM ± 0.1) a luoxetine, K i = 14.1 nm (EM ± 1.6) a a According to M.J. wens et al. (JPET 283: , 1997) Imipramine, Citalopram and luoxetine ERT activity, measured in similar conditions (rat cortex, [ 3 ]-citalopram), were: K i = 8.7 ± 0.04, 0.75 ± and 2.0 ± 0.1, respectively. 9
10 Table 1. Reference ligands. 3-Phenyltropanes Cocaine K i = 95 nm 1 AB-248 K i = 9.88 nm 2 AB-338 K i = 118 nm 3 β-ct K i = 63 nm 4 β-cpt-tartrate K i = 178 nm 5 I RTI-31 K i = 44.5 nm 6 RTI-32 K i = 23 nm 5 RTI-55 (β-cit) K i = 55 nm 7 RTI-83 K i = 2.6 nm 8 RTI-112 K i = 0.95 nm 9 RTI-121 K i = nm 10 I RTI-142 K i = 45nM 11 I RTI-311 K i = 30 nm 11 TCAs -1 K i = 0.58 nm 12 Amitriptyline K i = 0.88 nm 13 omipramine K i = 0.05 nm 13 Desipramine K i = 20 nm 14 Imipramine K i = 0.77 nm 15 Protriptyline K d = 19.6 nm 16 (R)-Trimipramine K d = 149 nm 16 10
11 Mazindols (R)-Mazindol K i = 103 nm 17 (R)-Mazindane K i = 13 nm 17 (R)-MAZ-10 K i = 82 nm 17 Br (R)-MAZ-85 K i = 413 nm 17 (R)-MAZ-89 K i = 1380 nm 17 Radioligands I 2 Br 403U76 K i = 55nM 18 4-ADAM K i = 1.46 nm 19 ADAM K i = 0.01 nm 20 AM K i = 1.04 nm 19 DAPA K i = 2.23 nm 21 2 I 2 I DAB K i = 1.1 nm 22 IDAM K i = 0.09 nm 22 MADAM K i = 0.25 nm 23 DAM K i = 0.12 nm 22 RIs 2 ()-Citalopram K i = 1 nm 24 Desmethyl-()- citalopram K i = 116 nm 25 Didesmethyl-()- citalopram K i = 194 nm 26 ()-LU K i = 14 nm 26 ()-LU K i = 47 nm (R)-luoxetine K i = 0.27 nm 13 Desmethyl-(R)- fluoxetine K i =26 nm 27 (R)-Venlafaxine K i = 3.81 nm 13 -desmethyl-(r)- venlafaxine K i = 40.2 nm 28 luvoxamine K i = 3.08 nm 29 11
12 ertraline K i = 0.79 nm 30 2 Desmethyl-sertraline K d = 3 nm 16 1 Bioorg. Med. Chem., 2009, 17: J. Med. Chem., 2005, 48:2758: J. eurochem., 2008, 105: J. Med. Chem., 2004, 47:6325: Bioorg. Med. Chem., 2009, 17: Bioorg. Med. Chem. Lett., 2003, 13: Bioorg. Med. Chem., 2007, 15: J. Med. Chem., 2002, 45: J. Med. Chem., 2003, 46: J. Med. Chem., 1995, 38: JPET, 2004, 308: Bioorg. Med. Chem., 2009, 17: The DrugMatrix Pharmacology data is a subset of the data freely available from the ational Toxicology Program. or more details see: 14 J. Med. Chem., 2010, 53: J. Med. Chem., 2011, 54: Eur. J. Pharm., 1997, 340: J. Biol. Chem., 1998, 273: J. Med. Chem., 2002, 45: J. Med. Chem., 2005, 48: Bioorg. Med. Chem. Lett., 2013, 23: J. Med. Chem., 2002, 45: J. Med. Chem., 2004, 47: J. Med. Chem., 2005, 48: Bioorg. Med. Chem. Lett., 2010, 20: PA, 2011, 108(29): J. Biol. Chem., 2004, 279: Bioorg. Med. Chem., 2009, 17: J Pharmacol Exp Ther., 2006, 318(2): J. Med. Chem., 2000, 43: Br. J. Pharmacol., 2009, 158:1:1 12
13 Table 2. Metrics-threshold optimisation details. ptimized pair metric-thresholds for each query and type of molecular fingerprint used in 2D fingerprint-based screening. fp; fingerprint. Query Metrics (threshold) 2D pharmacophore-based fp Chemical hashed fp RIs caled Tanimoto (> 0.59) Asymmetric Euclidean (< 4.10) Mazindols Asymmetric Tanimoto (> 0.83) Asymmetric Euclidean (< 5.80) TCAs Tanimoto (> 0.75) Asymmetric Tanimoto (> 0.85) Radioligands caled Tanimoto (> 0.93) Tanimoto (> 0.80) 3-phenyltropanes Euclidean (< 15) Tanimoto (> 0.75) luvoxamine Tanimoto (> 0.65) Asymmetric Tanimoto (> 0.60) luoxetine caled Tanimoto (> 0.59) Asymmetric Tanimoto (> 0.60) ertraline caled Tanimoto (> 0.89) Tanimoto (> 0.80) ()-citalopram caled Tanimoto (> 0.85) Tanimoto (> 0.80) General query Asymmetric Euclidean (< 19.57) Asymmetric Euclidean (< 4.88) 13
14 Table 3. ummary, in vitro screening. Results for compounds not evaluated in full binding assays. %: per cent inhibition of [ 3 ]-citalopram in a tested compound concentration of 1.66 x 10-6 M. V, virtual screening; 2L, hit-to-lead screening; A, Asinex; CB, ChemBridge; CD, ChemDiv; E, Enamine; LC, Life Chemicals. C01 Q Q Q R () 3 n Q = C,,, n= 1, 2, 3 T E V 23% E E V 8% T E V 0% T E V 19% T E V 12% T E V 28% CB V 35% T E 2L 1% BA A 2L 23% BA A 2L 34% BA A 2L 3% BA A 2L 21% BA A 2L 14% BA A 2L 51% CB 2L 0% CB 2L 0% CB 2L 0% CB 2L 12% CB 2L 17% CB 2L 29% CB 2L 23% CB 2L 29% CB 2L 32% CB 2L 16% CB 2L 13% CB 2L 41% CB 2L 37% CB 2L 40% CB 2L 0% CB 2L 5% CB 2L 55% CB 2L 28% CB 2L 0% CB 2L 4% CB 2L 25% C01 Q Q Q R () 3 n Q = C,,, n= 1, 2, CB 2L 45% CB 2L 37% CB 2L 7% CB 2L 40% CB 2L 12% CB 2L 21% CB 2L 53% CB 2L 36% CB 2L 16% CB 2L 12% CB 2L 9% CB 2L 10% T E 2L 8% T E 2L 53% T E 2L 11% T E 2L 27% T E 2L 24% T E 2L 44% T E 2L 0% E E 2L 36% E E 2L 55% C02 Q Q =,, A A V 14% T E 2L 9% A A 2L 4% T E 2L 0% T E 2L 0% T E 2L 27% T E 2L 5% T E 2L 5% T E 2L 33% 14
15 C03 ()n A A = C,,, n = 1, 2, 3 T E V 33% T E V 13% T E V 30% T E V 0% E V 23% T E V 11% T E V 0% T E V 0% T E V 3% CB 2L 0% CB 2L 7% CB 2L 29% CB 2L 0% CB 2L 0% CB 2L 0% CB 2L 2% CB 2L 0% CB 2L 0% E E 2L 22% E E 2L 26% E E 2L 0% E E 2L 26% C04 R 4 Q A () n R 3 A = C, Q =, C, n = 1, 2, CD V 0% T E V 20% A A 2L 0% A A 2L 0% T E 2L 14% T E 2L 10% T E 2L 0% T E 2L 41% T E 2L 42% E E 2L 50% T E 2L 6% C05 () n n = 0, CD V 4% CD V 0% C CD V 14% CB V 25% CB V 36% CB V 18% CB V 27% CB V 73% CB V 30% CB V 4% CB V 11% CB V 4% CB V 16% T E V 28% T E V 0% CB 2L 0% CB 2L 0% T E 2L 4% E E 2L 0% C07 E CD V 0% A A 2L 17% A A 2L 31% A A 2L 34% A A 2L 9% A A 2L 31% A A 2L 31% A A 2L 6% A A 2L 45% A A 2L 31% Y A 2L 45% R 3 15
16 C07 C09 Y A 2L 46% Y A 2L 50% C08 R 3 Q = C, () n = 0, 1, 2 n Q T E V 12% CD V 0% CD V 4% CB V 5% CB V 0% CB V 11% E E V 17% E E V 17% T E V 14% T E V 28% T E V 0% E E V 30% T E V 0% E E V 9% CB 2L 8% C09 C CD V 11% C CD V 5% C CD V 1% C CD V 15% C CD V 10% C CD V 2% C CD V 10% C CD V 11% C CD V 12% C CD V 21% C CD V 27% C CD V 12% C CD V 26% C CD V 34% C CD 2L 19% C CD 2L 27% C CD 2L 18% C10 T E V 0% T E V 5% T E V 15% G CD V 71% T E 2L 4% G CD 2L 29% G CD 2L 21% D CD 2L 0% D CD 2L 0% D CD 2L 4% T E 2L 34% T E 2L 25% T E 2L 9% T E 2L 14% T E 2L 21% T E 2L 20% T E 2L 29% T E 2L 32% T E 2L 8% T E 2L 21% T E 2L 0% T E 2L 16% T E 2L 29% T E 2L 17% T E 2L 12% T E 2L 50% T E 2L 8% T E 2L 26% T E 2L 4% T E 2L 27% T E 2L 19% 16
17 C10 C13 R 3 T E 2L 4% LC 2L 0% LC 2L 11% LC 2L 27% LC 2L 21% LC 2L 14% LC 2L 16% LC 2L 4% LC 2L 0% LC 2L 3% LC 2L 25% C11 R 3 R 4 T E V 27% T E 2L 5% T E 2L 0% T E 2L 7% T E 2L 10% C12 T E V 19% T E V 22% T E V 5% CD V 12% CB V 11% CB V 19% CB V 13% T E 2L 1% T E 2L 3% T E 2L 16% T E 2L 5% D CD V 4% C CD V 7% C CD V 15% CD V 0% CB V 16% CB V 8% CB V 7% CB V 14% CB V 3% CB V 10% CB V 11% CB V 11% BA A 2L 3% T E 2L 18% C14 Q = C, n = 0, 1 Q BA A V 15% BA A V 0% LC V 20% LC V 1% LC V 33% LC V 30% CD V 20% CD V 22% CD V 34% CD V 20% CB V 2% CB V 21% CB V 9% CB V 15% CB V 14% CB V 10% CB V 33% CB V 18% CB V 11% CB V 7% CB V 29% () n 17
18 C14 Q = C, n = 0, 1 () n Q CB V 14% C15 () n n = 0, 1 T E V 0% T E V 0% T E V 14% CD V 17% CD V 20% CB V 7% CB V 0% C17 Q Q Q Q () n Q = C, n = 0, 1 T E V 14% T E V 0% C24 R 3 T E V 11% T E V 21% CB V 19% T E V 16% T E V 14% C25 T E V 21% T E V 29% T E V 11% C CB V 6% CB V 8% C19 C27 R1 BA A V 2% BA A V 0% C21 () n n = 0,1 T E V 38% CB V 17% C23 D CD V 0% D CD V 9% D CD V 21% T E V 25% T E V 13% T E V 3% C28 T E V 23% T E V 17% C29 R CB V 14% 18
19 C30 R 3 T E V 15% CB V 15% CB V 20% C31 T E V 15% C CB V 27% C33 T E V 0% Br C CD V 0% C35 D CD V 6% C CB V 17% C37 T E V 35% 19
20 Table 4. ummary, in vitro full binding assays. %: per cent inhibition of [ 3 ]-citalopram in a tested compound concentration of 1.66 x 10-6 M (from screening). V, virtual screening; 2L, hit-to-lead screening; A, Asinex; CB, ChemBridge; CD, ChemDiv; E, Enamine; LC, Life Chemicals. The objective ranking of unique compounds with ICM VL score < -10 is shown. C01 tructure ID Path Vendor K i [nm] ± EM (%) Ranking A L A 90.5 ± 8.7 (69%) 196/ V CB ± 10.2 (36%) 119/740 E L E ± 2.3 (59%) 259/ V CB ± 17.9 (38%) 159/740 T L E 427 ± 23.7 (20%) 331/ L CB 609 ± 22.7 (44%) 189/1195 T L E ± 59 (39%) 311/ L CB ± 51 (26%) 167/ L CB 713. ± 49 (44%) 229/ L CB ± (31%) 196/1195 T L E 1200 ± 100 (14%) 315/ V CB 1800 ± (30%) 204/ L CB 2400 ± 60 (47%) 169/1195 T L E 3000 ± 25 (1%) 249/ L CB 3900 ± 200 (29%) 221/1195 Br T L E ± 1300 (24%) 322/1195 Br T L E >20,000 (5%) 324/1195 T L E >20,000 (35%) 228/1195 T L E >20,000 (57%) 325/
21 C02 tructure ID Path Vendor K i [nm] ± EM (%) Ranking T V E 336 ± 41.5 (46%) 568/740 T L E 1400 ± 40 (44%) 1169/1195 BA L A 1600 ± 57 (5%) 35/ L CB >10,000 (0%) - C03 tructure ID Path Vendor K i [nm] ± EM (%) Ranking L CB 926 ± 57 (33%) 932/ E V E ± 99.6 (33%) 509/ L CB 1000 ± 100 (42%) 935/ L CB 1800 ± 100 (45%) 942/1195 T L E >20,000 (22%) 100/ L CB >20,000 (8%) L CB >20,000 (6%) 941/ BA L A >20,000 (0%) 132/740 C04 tructure ID Path Vendor K i [nm] ± EM (%) Ranking T L E 1.5 ± 0.3 (54%) 991/1195 T V E 264 ± 11.1 (42%) 524/740 T V E 288 ± 15.2 (50%) 322/740 T L E 1000 ± 100 (46%) 1008/ V LC >10,000 (20%) 595/740 21
22 C05 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V CB 152 ± 12.7 (72%) - BA V A 1500 ± 50 (23%) 558/740 C06 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V CB 28.4 ± 0.3 (30%) 190/ V CB 42.5 ± 1.3 (49%) 12/ V CB ± 19.0 (43%) 36/ V CB 657 ± 43.0 (29%) 163/740 Br V CB ± 15.2 (22%) 57/740 Br V CB 1500 ± 27 (24%) 99/ V CB 2000 ± 70 (22%) 192/ V CB 2300 ± 78 (0%) 64/ V CB 2500 ± 45 (6%) 44/ V CD 3100 ± (12%) 323/740 Br 22
23 C07 tructure ID Path Vendor K i [nm] ± EM (%) Ranking Br V CB 50 ± 1.7 (52%) 203/ V CB 84 ± 3.7 (47%) 226/740 Br Y L A ± 10.7 (60%) 629/ V CB ± 22.7 (31%) 77/740 A L A 364 ± 12.6 (46%) 521/740 Y L A 441 ± 41.9 (56%) 455/740 Y L A 1100 ± 50 (38%) 466/740 A L A 1700 ± 60 (36%) 317/740 A L A 1700 ± 68 (40%) 188/740 C08 tructure ID Path Vendor K i [nm] ± EM (%) Ranking 2 BA L A 22.3 ± 2.8 (35%) 350/ L CB ± 1.0 (22%) 113/ V CB 321 ± 29 (47%) 51/ V CB 330 ± 32.0 (34%) 8/740 2 T V E 1200 ± 57.7 (16%) 2/740 2 BA V A >20,000 (11%) 41/740 23
24 C09 tructure ID Path Vendor K i [nm] ± EM (%) Ranking C V CD 86.1 ± 8.1 (63%) 373/740 C L CD 1000 ± 60 (32%) 668/740 C V CD 1100 ± 47.3 (24%) 305/740 C L CD >20,000 (32%) - C L CD >20,000 (0%) 962/1195 C10 tructure ID Path Vendor K i [nm] ± EM (%) Ranking T L E 127 ± 4.5 (30%) 477/1195 T L E 129 ± 9.8 (47%) 455/1195 T L E ± 15.5 (60%) 891/1195 Br L LC ± 3.2 (32%) 1/740 G V CD 802 ± 67 (1%) 20/740 Br T L E 1200 ± 50 (41%) 335/1195 G L CD 1300 ± 40 (10%) 461/1195 T L E 3500 ± 200 (38%) 572/1195 T L E 5000 ± 441 (45%) 480/1195 D L CD 13,000 ± 900 (32%) 400/1195 T L E >20,000 (17%) 913/
25 C11 tructure ID Path Vendor K i [nm] ± EM (%) Ranking T V E 56 ± 8.2 (45%) 100/740 C V CD 660 ± 61.8 (26%) - C V CD 3400 ± 300 (39%) - C12 tructure ID Path Vendor K i [nm] ± EM (%) Ranking + - T V E 268 ± 16 (40%) 734/740 T V E 790 ± 8.8 (37%) 70/740 T L E 3700 ± 200 (30%) 182/740 C13 tructure ID Path Vendor K i [nm] ± EM (%) Ranking E V E 322 ± 29 (39%) 288/740 T L E >20,000 (28%) 377/740 C14 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V LC 2300 ± (31%) 565/740 Br 25
26 C15 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V LC 2700 ± 200 (21%) 207/740 A V A >20,000 (0%) 165/740 C16 tructure ID Path Vendor K i [nm] ± EM (%) Ranking 2 BA V A 2300 ± 200 (6%) 4/ C17 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V LC >20,000 (0%) - C18 tructure ID Path Vendor K i [nm] ± EM (%) Ranking BA V A >20,000 (0%) 33/ C19 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V LC >20,000 (8%) 152/740 C20 tructure ID Path Vendor K i [nm] ± EM (%) Ranking A V A >20,000 (1%) 71/740 26
27 C21 tructure ID Path Vendor K i [nm] ± EM (%) Ranking V CD >20,000 (9%) 221/740 C22 tructure ID Path Vendor K i [nm] ± EM (%) Ranking E V E >20,000 (6%) 184/740 27
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