Supporting Information
Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers* and Elizabeth Yuriev* Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
*To whom correspondence should be addressed. D.K.C. Phone: +61 3 9903 9110. Fax: +61 3 9903 9582. E-mail:
[email protected]. E.Y. Phone: +61 3 9903 9611. Fax: +61 3 9903 9582. E-mail:
[email protected] 1
Table of Contents: Table S1. Summary of recent GPCR crystal structures
3
Table S2. Sequence homology and the ligands used in IFD
4
Table S3. Length of ECL2 for each receptor and the ECL2 sections used in the loop refinement protocol
5
Table S4. List of the active compounds docked during virtual screening
6
Table S5. Average ligand properties
16
Table S6. Enrichment factors for intermediate 5-HT2A models
17
Figure S1. Cognate ligand docking results
18
Figure S2. Schematic 2D plots of intermolecular interactions from IFD
19
References
21
2
Table S1. Summary of recent GPCR crystal structures. PDB ID
Resolution (Å)
Binding site
Ligand
ECL2
Ref.
Bovine Rhodopsin
1U19a
2.2
closed
cis-retinal
β-sheet
1
β2
2R4Rb
3.4/3.7c
-
carazololb
-
2
β2
2R4Sb
3.4/3.8c
-
carazololb
-
2
β2
3D4S
2.8
open
timolol
short helix 3
β2
2RH1
2.4
open
carazolol
short helix 4-5
β1
2VT4
2.7
open
cyanopindolol
short helix 6
Squid rhodopsin
2Z73
2.5
closed
cis-retinal
β-sheet
7
Squid rhodopsin
2ZIY
3.7
closed
cis-retinal
β-sheet
8
Opsin
3CAP
2.9
closed
-
β-sheet
9
Opsin
3DQB
2.7
closed
-
β-sheet
10
A2A
3EML
2.6
open
ZM-241,385
short helix 11
a
Highest resolution structure of rhodopsin chosen as example.
b
The orthosteric site and ECLs were not resolved in this structure.
c
3.4 Å in the plane of the membrane and 3.7 Å (or 3.8 Å) perpendicular to the plane of the membrane.
3
Table S2. Sequence identity between the GPCR targets and the rhodopsin, β2 and A2A templates measured over the transmembrane helical regions and the ligands used for IFD binding site refinement for each model. Receptor
% Homology
Ligand used for binding site refinement
rhodopsin
β2
A2A
A2A
25
34
100
-
β2
23
100
34
-
5-HT1B
23
41
35
cyanopindolol
5-HT2A
22
40
30
clozapine
5-HT2B
22
40
30
clozapine
5-HT2C
23
42
30
olanzapine
D2
26
41
37
olanzapine
D3
28
38
33
clozapine
D4
25
34
34
olanzapine
H1
21
37
34
cetirizine
M1
22
36
29
clozapine
4
Table S3. Length of ECL2 for each receptor. The sections of ECL2 used in the loop refinement protocol for each model (receptor numbering). Receptor
ECL2
Sections of ECL2 used in loop refinement
length
1
2
3
4
5-HT1B
17
189-193
194-199
200-205
193-200
5-HT2A
19
214-219
220-224
225-231
219-225
5-HT2B
21
194-200
201-207
208-214
200-208
5-HT2C
20
193-199
200-205
206-212
199-206
A2A
33
-
-
-
-
β2
23
-
-
-
-
D2
15
173-176
177-182
183-187
176-184
D3
13
173-176
177-180
181-185
176-182
D4
16
174-178
179-183
184-189
178-184
H1
22
166-173
174-180
181-187
173-181
M1
22
164-171
172-178
179-185
171-179
5
Table S4. List of all the active compounds docked into each model during virtual screening. Receptor Actives 5-HT1B
S O S N H
S
H N
NH2
N
N
N
S
N
O
OH
N cloperidone
Cl F
N N O
haloperidol
F
O Cl
N
N
N
fluphenazine
N
HO H N
O
OH O
F
N
ketanserin
O
loxapine
O HO H N
O
S
N H
H
N
S
H
N O
N
metergoline
F F
N
O
arotinolol
Cl
N
H
methysergide
N
metitepine
N
N HN
N
N
F
O ocaperidone
O pindolol OH
N O
N H
O propranolol OH
N N
F
N
risperidone
NH N
F
F
O
O
S N
N O
N
N H
N N sertindole
ritanserin
N O F
S
Cl N
N O N
S
NH N H
O O
F spiperone
N H H N
OH
H
N
O
tertatolol
NH
S
thioridazine
H O
OH O
yohimbine
S
S
N
N
N
Cl
Cl O N
ziprasidone
zotepine
6
5-HT2A
7
5-HT2B
8
5-HT2C
O H2N
NH H
O
N
N
Cl
Cl
N
N
OH N
chlorpromazine
buspirone NH N
S
Cl
O
N
S O
N N
fluphenazine
cyproheptadine
chlorprothixene
O
O N
N
N
N
amesergide
O
N F
O
NH
S
N
N
F
S
S
N
N
N O
N
O
N H
N
O ketanserin
loxapine
mesoridazine
S
H
methysergide
N H
N
metitepine
mianserin
F
H N
S O
Cl
N
N N
minaprine
mirtazapine
olanzapine S
S
S
N
N
N
N N
N
O
N F
pimozide N
N
F
promazine S N
N
N
O
propiomazine NH2
N
N
N
O
F
O
quetiapine
OH
O
O
N
N
N
N
N
N N
N
N
perphenazine
N
N N
N
N
O
N
N
HO
H
metergoline H S N
S
N
N
F
O
iloperidone O HO
O
N
N
O
H
N
N
NH
N O
N O
N
risperidone
F
Cl
SB206533
RS127445 F
ritanserin
NH
N
SB242084
O NH F
S
S
N N
N
O
N
N
NH
S
S
N
N
N thiethylperazine
spiperone
N
S
N
N
N Cl
N N
N N
tramadol
thioridazine S
N F
trazodone
N
N
Cl sertindole
O
O
O
F
N
OH
N
F F
Cl N O Cl
S trifluperazine
ziprasidone
N N H
O zotepine
9
F F
A2A
β2
10
D2
O H2N
O
N
H N
O S O
Cl N
N
N O
O
N H
HN amoxapine
amisulpride
N
O
N
N H
O O
F
HO
S
H
N
N
butaclamol
bromperidol
benperidol H N
S Cl
chlorpromazine
N
N Cl
OH O
NH
N
N H
clozapine
N H
N
N
N
chlorprothixene
O
N
N
Cl
N
O Cl
O
N H
domperidone S
O
Cl eticlopride
droperidol
S
F
F F
F F O F
N
OH
N
N N
HO fluanisone H N
fluphenazine
Cl N
isoclozapine
loxapine H N
melperone
N
N F
O N
N
F F
F
NH
Cl
penfluridol S
octoclothepin S
O S N O
N
N
Cl
N N
N
HO
N
N O
N
N F
N
F
ocaperidone S
Cl OH
N
nemonapride F
S
metoclopramide S
O
O
moperone
O
Cl
N
N H
N H
H2N
metitepine
O
N
N H
N
Cl
O molindone F
N
mesoridazine
OH O
N
O Cl
N
N
F
iloperidone
F
S
S O
N
N
N
S
N
O
N
N
O
haloperidol S
O
N
O
F
N
HO
flupenthixol
N
O N
N
N F
O
O
Cl
N
Cl
N
O F
O O
N
azaperone
N
F
O
F
OH
NH
N
N N
Cl
aripiprazole Br
O
Cl
F
pipothiazine
pimozide
perphenazine
N N
HO
prochlorperazine
F N
N N
OH O
Cl
N H
N
quetiapine
N
N
N H
O NH2 S O
O
N
N
N O
NH
N
Cl
risperidone S O S N O
N
F
sertindole
S
N
S
N
S N
S O
N O
N
N
S
N
F
N
N
N
N thioproperazine
N thiothixene
thioridazine
tiospirone O
trifluperazine
S
N
F
F F
N F
F F
Cl S
F
N
N
N
N trifluperidol
S
NH
OH
O
spiperone
O
O
N
O
NH
N O
N sulpiride
O
N
N
S O
F
O
O Cl raclopride
O HO
N
triflupromazine
ziprasidone
Cl
O N zotepine
11
F F
D3 H2N
O
OH
Cl
N
H N
O S O
N
O
N
O
HN amoxapine
bromperidol
OH O
NH
N
Cl
N H
O
Cl
O
N
H N O
fluspirilene O
haloperidol O
Cl N
iloperidone
F
S
S O Cl
N F
N
loxapine
melperone
F
F
O
NH N
N
N
OH
N
Cl
OH O
N
N
N
Cl
N H
N
N
O
N
N HO
promazine
N
Cl
O prochlorperazine
pipothiazine
perphenazine
S
S
N
N N
olanzapine
octoclothepin
HO pimozide
Cl
N
S
N
F
N N
O S N O
N
moperone S
Cl N
ocaperidone S
F
N
molindone H S N
N
O N
OH O
O
O
O
N nafadotride
O
N
metoclopramide
N N
isoclozapine
N N H
H2N
N
N
O iodosulpride
S N H
N
O
mesoridazine
O
N
N
H N
N
N
Cl
I
N
F
F
N
H N O S O
O
N
O
O
O
N
fluphenazine O
OH
N
N
HO
flupenthixol
eticlopride
F
F F
N
N
HO
domperidone
F
N
O
chlorpromazine
N
N
Cl
N H
F F
F
O
N
N
butaclamol S
S
N Cl
H
F benperidol
O
N
HN
NH
O
F
S
N H
O
N
N
N
amisulpride
HO
Br
O
quetiapine
raclopride
F
S
N N
N
F
O
O
N N
N
O
N NH
NH
O N
N
O
N H O
N O risperidone
Cl
S N
sulpiride
spiperone
N N
thioproperazine
O
S S
N F
N
N N
thioridazine
F
sertindole
O S N O
N
O NH2 S O
trifluperazine
O N
S
NH
OH
F F
F
F F
Cl S
N
N
N
Cl
O N
F trifluperidol
ziprasidone
zotepine
12
D4
OH
Cl
S
NH
H
N
N
O
F O
HN amoxapine
S Cl
Cl
N
F bromperidol
benperidol
N
chlorpromazine
butaclamol
chlorprothixene S
H N
O OH O
F
N
Cl
N H
N N
N
O
N H
N clozapine
F
O
N
HN
H N Cl N N
N
F
fluspirilene
N
N N
F
F
O
O Cl O
N
N
N
fluphenazine
O
O N
O
N
HO
fluperlapine
Cl OH
N
N
eticlopride
droperidol
F
N
N
F F
N
N
Cl
F O
N H
O
N
N
N N
HO
Br
O
haloperidol
iloperidone
isoclozapine
loxapine
S
S
N
S O
H N
O
N
OH O
N
N F
mesoridazine
ocaperidone
moperone S O
NH
N
Cl
N
OH O N
Cl
N H
N N
N pimozide
N
F
O
N
O
N O
Cl
N
F
perphenazine
octoclothepin N
Cl
N
N
O N
molindone F
S N
F
N
O
O
N
OH
N
N
F
Cl
risperidone
raclopride
prochlorperazine
S
S O O
N N
N
N NH
O
NH
N
N
O NH2 S O
N H
N
O S N O
S
O
O
N
N N
F
Cl sertindole S
spiperone
N F N N trifluperazine
O N
thiothixene S
NH
OH
F F
O thioridazine
sulpiride
F
F F
Cl S
N
N
N
Cl
O N
F trifluperidol
ziprasidone
zotepine
13
H1
F S
O
N
N
O O
N
N H
aceprometazine
Cl
N
O
O HN
Cl
N N astemizole
Br
Cl
azatadine
Cl
N
OH
N
N
O
azelastine Cl
N
O N
Cl
N
N
O
N
N
N
aripiprazole
N
bromodiphenhydramine S N
N
Cl
carbinoxamine Cl
buclizine
brompheniramine S
N
O
Br bepotastine
N N N
Cl N
N
N
OH Cl
N Cl
chlophedianol H N
N
N
chlorpromazine
chlorprothixene
chlorpheniramine
H N
N
O
cinnarizine
clemastine
Cl
Cl
N
N
N N
N
N N
N clozapine
HN
N cyproheptadine
cyclizine
N H
Br
desloratadine
desipramine
N
O
dexbrompheniramine
diphenhydramine
O O
HO
N N
O
N
O
N N
N diphenylpyraline
emedastine
doxylamine
N
epinastine
Cl OH
S N
N
F
N
Cl
flunarizine
N
O
N
N
N
OH
fexofenadine
O
F
O
NH2
N
N
doxepin
OH
N
N
N
OH
O
O
N
hydroxyzine
F
ketotifen
S
S
N
N
levocabastine
O
loratadine
S N
O N
N
N
N N
N
HN maprotiline H S N
Cl
methdilazine
mequitazine
meclizine
N
N
N
methotrimeprazine
mianserin S
O O
N
N
HO
N
olanzapine
mirtazapine S
N
N
N
NH N N
pemirolast
olopatadine
N
N O
N
N
N
N
N
N
N phenindamine
pheniramine
S
promethazine
promazine S
S
S N
OH
N
N O
N
N O HO
N
N
N propiomazine
S
OH N
N
thiethylperazine
trimeprazine
N terfenadine
quetiapine
O N S N
N N
NH N
N Cl
N N tripelennamine
triprolidine
ziprasidone
14
M1
O H
Cl O
N
O O
N
N
OH O
atropine Cl
O
benzquinamide
HO
Cl
Cl
N
O
chlorprothixene
N
N
OH O
clidinium
cyclopentolate
cyclizine O
S
H N
OH
O
N
O
N+
N
chlorpromazine
carbinoxamine
buclizine
biperiden
S
N
O
N
OH
benztropine
S N
N
N N
O H
N
O
N N O
cycrimine
N N
O dicyclomine
desipramine
diphenidol
N
O
OH
N
HN
N dosulepin
doxylamine
doxepin
S O
N O N
N
O
HO
O
ethopropazine S
N+ N+ Br-
O
flavoxate
N
O
O
O
OH
O
O
homatropine methyl bromide H S N
glycopyrrolate
S
N
O
O
OH
methantheline
hyoscyamine O OH
O
O
Cl N
H2N
N
N
N H
N+
O
O
N N
O
O
N
N
N metoclopramide O NH
metixene
methotrimeprazine
N
N O
O
N
OH O
N
OH O
olanzapine
oxybutynin O
S
S
N
N
O
+
orphenadrine
N
N
O
N
OH
O N+
N
N
N oxyphencyclimine
oxyphenonium N
S
pirenzapine
NH
O O
H N
H
N
N
N
O
O
O N
quinacrine S N
N+
F
F F
N N
thiethylperazine
tolterodine
O N N
OH
OH
N solifenacin
scopolamine
S
O
H
N propiomazine
propantheline
promethazine S
HO
O N
promazine
procyclidine
Cl
OH
OH O
N tridihexethyl
triflupromazine
trihexyphenidyl
tropsium
15
Table S5. Average ligand properties calculated in QikProp12 (average shape Tanimoto score, calculated in ROCS13 and average 2D Tanimoto score calculated using UNITY in Sybyl14). Property/ Receptor
Molecular Rotatable Weight Bonds (g/mol)
PSA Calc H-bond logP Donor (Å2)
H-bond Solvent Shape Acceptor Accessible Tanimoto Volume Scorea 3 (Å )
2D Tanimotoa Score
5-HT1B
369
4.6
54.7
3.8
1.1
5.3
1185
0.52
0.29
5-HT2A
376
4.1
44.0
4.2
0.6
5.1
1211
0.48
0.27
5-HT2B
356
3.5
50.4
3.8
0.9
5.1
1162
0.48
0.26
5-HT2C
362
3.6
39.9
4.1
0.5
4.8
1167
0.53
0.25
A2A
344
5.0
88.5
2.9
1.3
6.3
1075
0.54
0.24
β2
301
8.2
63.2
2.4
2.5
5.4
1055
0.54
0.53
D2
378
4.6
46.9
4.1
0.7
5.4
1198
0.50
0.25
D3
381
4.8
49.0
3.9
0.8
5.5
1193
0.51
0.30
D4
375
4.0
44.1
4.1
0.7
5.1
1179
0.52
0.26
H1
328
4.1
27.4
4.0
0.4
3.9
1095
0.61
0.33
M1
320
4.9
29.5
4.0
0.4
4.0
1087
0.61
0.23
decoysb
360
5.5
86.7
3.1
1.9
5.8
1117
0.48
0.22
a
Score of 0 indicates dissimilar ligands, maximum score of 1 indicates identical ligands.
b
Schrödinger decoy library.15
16
Table S6. Enrichment factors for intermediate 5-HT2A models at x% of the ranked database screened (maximum enrichment factors at 2% 21.4; 5% 19.8; 10% 10, of the ranked database screened). Model
Enrichment factor (at x% of the ranked database screened) 2%
1
5%
10%
Enrichment factor
Number of Enrichment compounds factor recovered
Number of Enrichment compounds factor recovered
Number of compounds recovered
2.0
2
2.8
7
3.3
16
3.1
3
2.4
6
2.9
14
13.3
13
7.7
19
4.7
23
6.1
6
6.9
17
5.9
29
(Initial) 2 (After loop refinement) 3 (After IFD) 4 (Final)
17
Figure S1. Cognate ligand docking results; crystal structure shown in blue, docked pose shown in orange (docking method in brackets). a) carazolol from 2RH1 crystal structure compared to docked pose of carazolol (Glide XP), b) timolol from 3D4S crystal structure compared to docked pose of timolol from virtual screening (Glide XP) and c) ZM-241,385 from 3EML crystal structure compared to docked pose of ZM-241,385 (Glide XP, with crystal structure water). This image was created in PyMOL.16
18
Figure S2. Schematic 2D plots of intermolecular interactions in the docked structures from IFD. a) cyanopindolol docked into the 5-HT1B receptor, b) clozapine docked into the 5-HT2A receptor, c) clozapine docked into the 5-HT2B receptor, d) olanzapine docked into the 5-HT2C receptor, e) olanzapine docked into 19
the D2 receptor, f) clozapine docked into the D3 receptor, g) olanzapine docked into the D4 receptor, h) cetirizine docked into the H1 receptor, i) clozapine docked into the M1 receptor. Hydrogen atoms omitted for clarity. Non-bonded interactions: vdW, red spokes; hydrogen bonds, dashed greenlines. Covalent bonds: ligand, purple; protein, brown. Protein: side-chains are shown only for residues, to which a ligand is hydrogen bonded; a red single spoked arcs show residues involved only in vdW contact(s) with a ligand. Atoms: carbon, black; oxygen, red; nitrogen, blue; sulphur, yellow; chlorine; green. The plots were created with the program LIGPLOT.17
20
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