Homology Modeling and Docking Evaluation of Aminergic G Protein

Telephone: +61 3 9903 9110 (D.K.C.) and +61 3 9903 9611 (E.Y.). Fax: +61 3 9903 9582 (D.K.C.) and +61 3 9903 ... Of the nine homology models developed...
0 downloads 3 Views 1MB Size
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

References (1)

Okada, T.; Sugihara, M.; Bondar, A.-N.; Elstner, M.; Entel, P.; Buss, V. The retinal conformation

and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J. Mol. Biol. 2004, 342, 571-583. (2)

Rasmussen, S. G. F.; Choi, H.-J.; Rosenbaum, D. M.; Kobilka, T. S.; Thian, F. S.; Edwards, P. C.;

Burghammer, M.; Ratnala, V. R. P.; Sanishvili, R.; Fischetti, R. F.; Schertler, G. F. X.; Weis, W. I.; Kobilka, B. K. Crystal structure of the human β2 adrenergic G-protein-coupled receptor. Nature 2007, 450, 383-387. (3)

Hanson, M. A.; Cherezov, V.; Griffith, M. T.; Roth, C. B.; Jaakola, V.-P.; Chien, E. Y. T.;

Velasquez, J.; Kuhn, P.; Stevens, R. C. A specific cholesterol binding site Is established by the 2.8 Å structure of the human β2-adrenergic receptor. Structure 2008, 16, 897-905. (4)

Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A.; Rasmussen, S. G. F.; Thian, F. S.; Kobilka, T. S.;

Choi, H.-J.; Yao, X.-J.; Weis, W. I.; Stevens, R. C.; Kobilka, B. K. GPCR engineering yields highresolution structural insights into β2-adrenergic receptor function. Science 2007, 318, 1266-1273. (5)

Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G. F.; Thian, F. S.; Kobilka, T. S.;

Choi, H.-J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. High-resolution crystal structure of an engineered human β2-adrenergic G protein coupled receptor. Science 2007, 318, 1258-1265. (6)

Warne, T.; Serrano-Vega, M. J.; Baker, J. G.; Moukhametzianov, R.; Edwards, P. C.; Henderson, R.;

Leslie, A. G. W.; Tate, C. G.; Schertler, G. F. X. Structure of a β1-adrenergic G-protein-coupled receptor. Nature 2008, 454, 486-491. (7)

Murakami, M.; Kouyama, T. Crystal structure of squid rhodopsin. Nature 2008, 453, 363-367.

(8)

Shimamura, T.; Hiraki, K.; Takahashi, N.; Hori, T.; Ago, H.; Masuda, K.; Takio, K.; Ishiguro, M.;

Miyano, M. Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J. Biol. Chem. 2008, 283, 17753-17756. 21

(9)

Park, J. H.; Scheerer, P.; Hofmann, K. P.; Choe, H.-W.; Ernst, O. P. Crystal structure of the ligand-

free G-protein-coupled receptor opsin. Nature 2008, 454, 183-187. (10) Scheerer, P.; Park, J. H.; Hildebrand, P. W.; Kim, Y. J.; Krausz, N.; Choe, H.-W.; Hofmann, K. P.; Ernst, O. P. Crystal structure of opsin in its G-protein-interacting conformation. Nature 2008, 455, 497-502. (11) Jaakola, V.-P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y. T.; Lane, J. R.; Ijzerman, A. P.; Stevens, R. C. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008, 322, 1211-1217. (12) QikProp, version 3.1; Schrödinger, LLC: New York, NY, 2008. (13) ROCS, version 2.3.1; OpenEye Scientific Software Inc.: Santa Fe, New Mexico, 2007. (14) Sybyl-X, version 1.0; Tripos: St. Louis, MO, 2009. (15) Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749. (16) DeLano, W. L. The PyMOL molecular graphics system, DeLano Scientific: Palo Alto, CA, USA, 2002. (17) Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8, 127-134.

22