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Synthesis of Succinamide Backbone Derivatives as Prolyl Endopeptidase Inhibitors.

Synthesis of Succinamide Backbone Derivatives as Prolyl Endopeptidase Inhibitors.

CONTENTS

1.

........................................................................................................1

2.

............................................................................................................4

2.1 ........................................................................................4 2.2 ......................................................................................................5 2.2.1 Virtual Screening..............................................................................5 2.2.2 New scaffold design.........................................................................9 2.2.3 R1, R2 group ...............................................................13 2.2.4 R3 group ......................................................................25 2.2.5 Enzyme assay..................................................................................35

3. ....................................................................................................373.1 PEP ....................................................................................37 3.2 Enzyme assay ..................................................................................39

4.

..........................................................................................................45

5. ...........................................................................................................46

6. ...........................................................................................................49

Abstract ..........................................................................................................51

List of TablesTable 1. R1 group Libdock score..................................................................7 Table 2. R2 group Libdock score..................................................................8 Table 3. Method of PEP assay.....................................................................36 Table 4. PEP inhibitory activities of the synthesized compounds............39

List of FiguresFig. 1. The proposed binding site of Phenylpropylcarbonyl-L-Tic pyrrolidine.......................................................................................................2 Fig. 2. Key interactions between inhibitors and PEP ................................3 Fig. 3. PEP protein structure.........................................................................5 Fig. 4. Active site and docking sphere .......................................................6 Fig. 5. trans-4-(aminomethyl)cyclohexanecarboxylic acid Z-pro-prolinal Libdok position................................................................................7 Fig. 6. 2,2-Diphenylethylamine Z-pro-prolinal Libdok position.............8 Fig. 7. New scaffold design..........................................................................10 Fig. 8. UV-Vis ...............................................................................35 Fig. 9. 1H-NMR spectrum of (PEP-33) .....................................................49 Fig. 10. Fig. 12.13 1

C-NMR spectrum of (PEP-33) ..................................................49 C-NMR spectrum of (PEP-36) ..................................................50

Fig. 11. H-NMR spectrum of (PEP-36) ...................................................5013

List of SchemesScheme 1. Scheme 2. Scheme 3. .................................................................................................11 .................................................................................................12 .................................................................................................12

ABBREVIATIONS

(Boc)2O CHCl3 DMF DMSO DS EA EDC Hex HOBT LiOH MC MeOH MgSO4 NaHCO3 NMR PEP TEA TFA TFAA THF TLC TMSCl UV-Vis

-

Di-tert-butyl dicarbonate Chloroform N,N-Dimethylformamide Dimethyl sulfoxide Discovery Studio 2.0 Ethyl acetate 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide Hexane 1-Hydroxybenzotriazole Lithium hydroxide Methylene chloride Methanol Magnesium sulfate Sodium bicarbonate Nuclear magnetic resonance spectroscopy Prolyl endopeptidase Triethylamine Trifluoroacetic acid Trifluoroacetic anhydride Tetrahydrofuran Thin layer chromatography Chlorotrimethylsilane Ultraviolet-Visible spectroscopy

1.

20 amino acid cyclic structure proline peptidase peptide protein folding peptide .1~3) Prolyl

endopeptidase (PEP, EC 3.4.21.26) 30 amino acids peptides proline carboxyl side proline-specific serine peptidase 1971 walter4) oxytocin-cleaving enzyme , .5~7) PEP , , , , , .8) PEP vasopressin, substance P, thyrotropin-releasing hormone (TRH) proline neuropeptide 9), vasopressin , substance P -amyloid neurotoxicity . cognition-enhancing neuropeptides PEP PEP .10~12) Porcine brain PEP crystal structure PEP 50, 60 , 80kDa size . PEP / hydrolase fold seven-blade -propeller domain , seven-blade -propeller domain gate enzyme selectivity .13) PEP Z-Pro-prolinal complex 3 S1, S2, S3 pocket , Ser554, His680, Asp641 residue .14) S1, S2, S3 pocket Phenylproplycarbonyl-L-Tic-pyrrolidine inhibitor PEP binding .(Fig 1.)15)

- 1 -

Fig 1. The proposed binding site of Phenylpropylcarbonyl-L-Tic-pyrrolidine S1 pocket hydrophobic residue Trp595, Phe476, Val644, Val580, Trp599 pocket hydrophobic , proline specific pocket. proline specificity Trp595 indole ring ring stacking15) . S1 pocket PEP enzyme residue Ser554 PEP inhibitor design pocket . Fig 2 S1 pocket Ser554 inhibitor interaction PEP inhibitor key interaction .13)

S2 pocket pocket . Asn534, Tyr453, Arg618 residue 16), S2 pocket inhibitor P2 position Trp595 Arg643 hydrogen bond interaction , Fig 1 Fig 2 . S3 pocket Phe173, Met235, Cys255, Ile591, Ala594 nonpolar residue hydrophobic .15) S3 pocket pocket S3 pocket size .

- 2 -

Fig 2. Key interactions between inhibitors and PEP

PEP enzyme , , inhibitor , dipeptide bond succinamide , S1, S2, S3 pocket R3, R1, R2 group PEP inhibitor , , . PEP inhibitor .

- 3 -

2. 2.1 Sigma-Aldrich(St.Louis, U.S.A), Merck (Darmstadt, Germany), TCI(Tokyo, Japan), Lancaster(Manchester, England) . Assay PEP enzyme(isolated from Flavo bacterium sp) Seikagaku Co.(Tokyo, Japan) , Substrate

Seikagaku Co.(Tokyo, Japan) Bachem (Dubendorf, Switzerland) . TLC(Thin Layer Chromatography) Merck silica gel 60 F254 , TLC UV-lamp

phosphomolybdic acid(PMA) . Flesh column chromatography Merck silica gel 230~400mesh .

PEP inhibitor Docking activity Docking structure Virtual screening Computer Cambridge

Software Chemoffice Accelrys Software Discovery Studio 2.0 (DS 2.0) version , 1 13

H-NMR (400MHz),

C-NMR (100MHz) NMR spectra Inovia AS400

Varian NMR

H-NMR (600MHz),

C-NMR (1500MHz) NMR spectra

bruker AVANCE 600 NMR . . Chemical shift TMS(tetramethylsilane) -unit , . Chemical shift (integrated

intensity, multiplicity). multiplicity splitting pattern s(singlet), d(doublet), t(triplet), m(multip- let) . Enzyme assay UV-Vis spectrometer Varian CARY 300 Bio , EI MS JEOL JMS-700 .

- 4 -

2.2 2.2.1 Virtual Screening 2.2.1.1 PEP protein structure PEP inhibitor docking computer . PEP protein structure Protein Data Bank (PDB) . PDB PEP protein structure mutant . PEP protein structure Z-pro-prolinal inhibitor 1h2y .

Fig. 3. PEP protein structure PDB PEP protein structure protein glycerol , glycerol . glycerol , PEP protein structure inhibitor Z-pro-prolinal . PEP protein structure docking 10 docking sphere

- 5 -

, substrate inhibitor interaction amino acid amino acid . Figure 4. active site docking sphere .

Fig. 4. Active site and docking sphere

2.2.1.2 Virtual screeningPEP protein inhibitor PEP inhibitor . pocket docking activity virtual screening . inhibitor inhibitor Z-pro-prolinal inhibitor standard . R1 group inhibitor P2 position P3 position linker . phenyl ring amino acid cyclohexane, pipearazine 7 amino acid R1 group virtual screening . R1 group trans-4-(aminomethyl)cyclohexanecarboxylic acid

- 6 -

docking score 107.258 , standard Z-pro-prolinal docking score 104.173 .

Fig. 5. trans-4-(aminomethyl)cyclohexanecarboxylic acid Z-pro-prolinal Libdok position phenyl ring linker trans-4-(aminomethyl)cyclohexanecarboxylic acid

R1 group , inhibitor PEP . amino acid carboxylic acid methyl ethyl carboxylate .R1 group trans-4-(Aminomethyl)cyclohexanecarboxylic acid 4-Aminomethylbenzoic acid cis-4-Aminocyclohexanecarboxylic acid 4-Aminobenzoic acid 3-Aminobenzoic acid Ethyl piperazinoacetate Isonipecotic acid Z-pro-prolinal Absolute energy 22.964 37.223 15.45 46.317 41.023 33.901 23.665 38.971 Relative energy 10.602 14.038 1.956 17.898 12.326 12.048 7.288 9.354 LibDock score 107.258 105.99 105.724 97.281 95.754 95.191 94.825 104.173

Table 1. R1 group Libdock score

- 7 -

trans-4-(aminomethyl)cyclohexanecarboxylic acid R1 group R2 group virtual screening . R2 group inhibitor P3 position PEP enzyme hydrophobic S3 pocket interaction . P3 position hydrophobic S3 pocket

aromatic group . R2 group inhibitor aromatic amine cycloalkyl, aliphatic, hetero cyclic amine 80 amine virtual screening . R2 group Docking 2,2-diphenylethylamine docking score 135.768 , standard Z-pro-prolinal docking score 104.173 score .

Fig. 6. 2,2-Diphenylethylamine Z-pro-prolinal Libdok position 80 amine 20~30% score 27 amine R2 group .R2 group 2,2-Diphenylethylamine 1-Ethylpiperazine 3-(Aminomethyl)pyridine Absolute energy 45.473 32.293 38.81 Relative energy 2.25 7.604 10.539 LibDock score 135.768 123.141 122.897

- 8 -

N-Methylphenethylamine 2-Fluorobenzylamine 4-Fluoro--methylbenzylamine 2-(p-Tolyl)ethylamine 3-Methoxybenzylamine 4-Fluoroaniline (S)-(+)-1-Cyclohexylethylamine 2-Methoxybenzylamine 3-Methoxypropylamine Isoamylamine 3,3-Dimethylbutylamine sec-Butylamine 2-(2-Aminoethyl)pyridine 4-Fluorophenethylamine 3-Methylbenzylamine 4-Fluorobenzylamine Cyclopropanemethylamine Amylamine N-Octylamine N-Butylamine Pyrrolidine Aniline Benzylamine Cyclohexylamine Z-pro-prolinal

44.941 35.509 40.965 36.539 45.49 42.22 25.506 43.765 26.403 26.233 26.233 28.682 44.757 34.823 33.555 41.08 20.611 22.458 19.341 21.439 26.941 41.29 33.07 21.317 38.971

16.682 7.531 12.438 9.839 10.75 5.982 6.486 8.403 9.81 6.765 6.785 9.49 17.206 9.608 5.49 12.936 4.355 5.624 2.956 4.016 2.681 6.144 5.214 5.425 9.354

122.713 118.809 118.641 118.521 117.045 116.757 116.098 116.096 114.792 113.876 113.876 113.204 112.853 111.916 111.34 111.245 109.991 109.818 109.637 108.125 106.757 98.631 97.589 95.011 104.173

Table 2. R2 group Libdock score

2.2.2 New scaffold design PEP protein S1, S2, S3 pocket inhibitor virtual screening R1, R2 group scaffold inhibitor .

- 9 -

Fig. 7. New scaffold design

Inhibitor P1 position proline specific pocket S1 pocket . proline piperidine, azepane ring size proline ring pyrrolidine ring . proline modify activity . Proline 2 PEP enzyme residue serine554 proline 2 reactive functional group catalytic active site interaction potency . P1 position pyrrolidine 2(S)-cyanopyrrolidine, L-prolinol, L-prolinal, L-prolinamide, L-proline methyl ester . P2 position proline group . proline chain natural amino acid inhibitor , nonnatural amino acid inhibitor .17~18) Ring proline chain

- 10 -

natural amino acid 4 dipeptide bond . chain L-leucine dipeptide bond succinic acid . S2 pocket S3 pocket P2 position P3 position linker R1 group . R1 group virtual screening phenyl group cycloalkyl amino acid trans-4-(aminomethyl)cyclohexanecarboxylic acid . S3 pocket hydrophobic , P3 position aromatic group . R2 group amine virtual screening , aromatic aliphatic, cycloalkyl, heterocyclic amine amine . R1 group Scheme 1 , R1 group trans-4-aminomethylcyclohexanecarboxylic acid R2 group amine scheme 2 . R1 group trans-4-aminomethylcyclohexanecarboxylic acid R2 group 2,2-diphenylethylamine Reactive functional group R3 scheme 3 .

Scheme 1.

- 11 -

Scheme 2.

Scheme 3.

- 12 -

2.2.3 R1, R2 group synthesis 2.2.3.1 methyl 4-oxo-4-(pyrrolidin-1-yl)butanoate

mono-Methyl succinate(5g, 37.8mmol) TEA(5.8ml, 41.6mmol) MC 60ml , 0 MC pivaloyl chloride(4.66ml, 37.8mmol) dropwise 0 1 . 1 MC 20ml Pyrrolidine(3.44ml, 41.6mmol) TEA(5.8ml, 41.6mmol) 0 dropwise 24 . TLC MC 30% citric acid, brine, saturated NaHCO3(aq) MgSO4 . EA flesh column chromatography Methyl 4-oxo-4-(pyrrolidin-1-yl)butanoate(6.1g, 3.29 mmol) .19)

Yield : 87% Rf : 0.68 (MeOH:EA=1:2)1

H-NMR (CDCl3, 400MHz) : 3.69 (3H, s), 3.46 (4H, t, J=7.2Hz), 2.68 (2H, t, J=6Hz), 2.58 (2H, t, J=6.8Hz), 1.94~2.01 (2H, m), 1.83~1.90 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 173.26, 169.27, 51.46, 46.19, 29.12, 27.27, 25.84

- 13 -

2.2.3.2 4-oxo-4-(pyrrolidin-1-yl)butanoic acid

Methyl 4-oxo-4-(pyrrolidin-1-yl)butanoate(6.4g, 34.55mmol) 30% MeOH 50ml , LiOH(1g, 41.46mmol) 4 . TLC MC starting . 10% HCl(aq) pH3 . MC MgSO4 . 4-oxo-4-(pyrrolidin-1-yl)butanoic acid(4.6g, 26.87mmol ) .19)

Yield : 78% Rf : 0.29 (MeOH:EA=1:2)1

H-NMR (CDCl3, 400MHz) : 3.41 (4H, t, J=7.2Hz), 2.64 (2H, t, J=6Hz), 2.56 (2H, t, J=6.8Hz), 1.89~1.95 (2H, m), 1.78~1.85 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 175.66, 170.57, 46.71, 29.45, 25.92, 24.31

2.2.3.3

(1R,4R)-methyl

4-(aminomethyl)cyclohexanecarboxylate

- 14 -

trans-4-(Aminomethyl)cyclohexanecarboxylic acid(4g, 26.4mmol) TMSCl(6.7ml, 52.9mmol) MeOH 22ml 12 . TLC product (1R,4R)methyl 4-(aminomethyl)cyclohexanecarboxylate(4.4g, 25.7mmol) HCl salt .20)

Yield : 97% Rf : 0.11 (Hex:EA=2:1)1

H-NMR (CDCl3, 400MHz) : 3.64 (3H, s), 2.83 (2H, t, J=6.4Hz), 2.18~2.36 (1H, m), 1.97~2.04 (2H, m) 1.84~1.95 (2H, m), 1.72~1.73 (1H, m), 1.43~1.47 (2H, m), 1.03~1.07 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 175.57, 51.65, 45.42, 42.67, 35.29, 29.44, 28.00

2.2.3.4 (1R,4R)-methyl 4-((4-oxo-4-(pyrrolidin-1-yl)butanamido)methyl)cyclohexanecarboxylate

4-oxo-4-(pyrrolidin-1-yl)butanoic acid(2.5g, 14.6mmol) TEA(2.24ml, 16.06mmol) MC 50ml , 0 MC pivaloyl chloride(1.8ml, 14.6mmol) dropwise 0 1 . 1 0 TEA(6.7ml, 48.18mmol), (1R,4R)-methyl 4-(amino methyl)cyclohexanecarboxylate(2.75g, 16.06mmol) 24 . TLC MC 30% citric acid, brine, saturated NaHCO3(aq) MgSO4 . MeOH EA (1:2) flesh

- 15 -

column chromatography (1R,4R)-methyl 4-((4-oxo-4-(pyrrolidin-1yl)butanamido)methyl)cyclohexanecarboxylate(3.8g, 11.7mmol) .19)

Yield : 80% Rf : 0.625 (MeOH:EA=1:2)1

H-NMR (CDCl3, 400MHz) : 6.81 (1H, s), 3.60 (3H, s), 3.35 (4H, t,

J=7.2Hz), 2.98 (2H, t, J=6.4Hz), 2.51 (2H, t, J=6Hz), 2.46 (2H, t, J=6.8Hz), 2.11~2.13 (1H, m), 1.87~1.90 (2H, m), 1.84~1.87 (2H, m),1.76~1.78 (2H, m), 1.73~1.75 (2H, m), 1.33~1.34 (1H, m) 1.27~1.31 (2H, m) 0.84~0.87 (2H, m)13

C-NMR (CDCl3, 100MHz) : 176.04, 172.40, 170.26, 51.41, 46.42, 45.67, 43.02, 37.18, 31.22, 30.29, 28.36, 25.92, 24.27

- 16 -

2.2.3.5 R1 derivatives Scheme 1 R1 derivatives .

- 17 -

2.2.3.6 (1R,4R)-4-((4-oxo-4-(pyrrolidin-1-yl)butanamido)methyl)cyclohexanecarboxylic acid

(1R,4R)-methyl 4-((4-oxo-4-(pyrrolidin-1-yl)butanamido)methyl)cyclohexanecarboxylate(3.6g, 11.1mmol) 30% MeOH 60ml , LiOH (320mg, 13.3mmol) 24 . TLC , MC starting . 10% HCl(aq) pH3 . MC MgSO4 . MeOH EA (1:8) flesh column

chromatography

(1R,4R)-4-((4-oxo-4-(pyrrolidin-1-yl)butanamido)-

methyl)cyclohexa necarbxylic acid(3.2g, 10.3mmol) .19)

Yield : 93% Rf : 0.548 (MeOH:EA=1:2)1

H-NMR (CDCl3, 400MHz) : 6.81 (1H, s), 3.41 (4H, t, J=7.2Hz,), 3.10 (2H, t, J=6.4Hz), 2.59 (2H, t, J=6Hz), 2.52 (2H, t, J=6.8Hz), 2.18~2.22 (1H, m), 1.97~2.01 (2H, m), 1.84~1.87 (2H, m), 1.76~1.78 (2H, m), 1.73~1.75 (2H, m), 1.33~1.34 (1H, m) 1.27~1.31 (2H, m) 0.84~0.87 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 179.79 172.83, 170.71, 46.72, 45.98, 43.02, 37.23, 31.50, 30.58, 28.47, 26.01, 24.39

- 18 -

2.2.3.7

(1R,4R)-N-(2,2-diphenylethyl)-4-((4-oxo-4-(pyrrolidin-1-

yl)butanamido)methyl)cyclohexanecarboxamide

(1R,4R)-4-((4-oxo-4-(pyrrolidin-1-yl)butanamido)methyl)cyclohexanecarboxylic acid(62mg, 0.199mmol) MC 5ml , EDC(50mg, 0.26mmol), HOBT(41mg, 0.3mmol) , 1 . 1 TEA(84, 0.6mmol), 2,2-Diphenylethylamine(40mg, 0.199mmol) 24 . TLC , MC , MC 30% citric acid, brine, saturated NaHCO3(aq) . MgSO4 MeOH MC (1:8) flesh column chromatography (1R,4R)-N-(2,2-diphenylethyl)-4-((4-oxo-4(pyrrolidin-1-yl)butanamido)methyl)cyclohexanecarboxamide(66mg, 0.135mmol) .

Yield : 68% Rf : 0.57 (MeOH:EA=1:2)1

H-NMR (CDCl3, 400MHz) : 7.28~7.32 (4H, m), 7.19~7.23 (6H, m), 6.64 (1H, s), 5.50 (1H, s) 4.19 (1H, t, J=8Hz,), 3.86 (2H, t, J=6Hz), 3.41 (4H, t, J=7.2Hz), 3.03 (2H, t, J=6.4Hz), 2.58 (2H, t, J=6Hz), 2.52 (2H, t,

J=6.8Hz), 2.18~2.22 (1H,

m),

1.91~2.97

(2H,

m),

1.83~1.88 (3H, m), 1.71~1.77 (4H, m), 1.35~1.38 (1H, m) 1.31~1.34 (2H, m) 0.85~0.89 (2H, m)13

C-NMR (CDCl3, 100MHz) : 175.51, 172.50, 170.28, 141.66, 128.51,

- 19 -

127.88, 126.63, 50.44, 46.49, 45.24, 43.50, 37.20, 31.39, 30.44, 28.87, 26.00, 24.36

2.2.3.8 R2 derivatives Scheme 2 R2 derivatives .

- 20 -

- 21 -

- 22 -

- 23 -

- 24 -

2.2.4 R3 group synthesis 2.2.4.1 (1R,4R)-methyl 4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylate

(1R,4R)-methyl 4-(aminomethyl)cyclohexanecarboxylate(1g, 5.84mmol) MeOH 50ml , 0 NaHCO3(980mg, 11.7mmol), (Boc)2O (1.4g, 6.42mmol) 5 . TLC , EA brine . MgSO4 Hex EA (2:1) flesh column chromatography (1R,4R)-methyl 4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylate(1.3g, 4.79mmol ) . Yield : 82% Rf : 0.53 (Hex:EA=2:1)1

H-NMR (CDCl3, 400MHz) : 3.61 (3H, s), 2.92 (2H, t, J=6.4Hz), 2.15~2.21 (1H, m), 1.93~1.96 (2H, m), 1.75~1.80 (2H, m), 1.38 (9H, s), 1.32~1.34 (2H, m), 1.31~1.32 (1H, m), 0.89~0.96 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 176.12, 155.59, 79.02, 51.52, 46.52, 43.16, 37.69, 29.67, 28.45, 28.41

- 25 -

2.2.4.2 (1R,4R)-4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylic acid

(1R,4R)-methyl 4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylate(1.1g, 4.05mmol) 30% MeOH 50ml , LiOH(116mg, 4.8 6mmol) 24 . TLC EA starting . 10% HCl(aq) pH3 . EA MgSO4 . (1R,4R)-4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylic acid(986mg, 3.83mmol) .19) Yield : 95% Rf : 0.484 (MeOH:MC=1:8)1

H-NMR (CDCl3, 400MHz) : 2.94 (2H, t, J=6.4Hz), 2.18~2.25 (1H, m), 1.99~2.02 (2H, m), 1.78~1.81 (2H, m), 1.38 (9H, s),

1.34~1.35 (2H, m), 1.31~1.32 (1H, m), 0.91~0.98 (2H, m)13

C-NMR (CDCl3, 100MHz) : 181.47, 155.96, 79.18, 51.52, 46.52, 43.07, 37.67, 29.61, 28.44, 28.30

- 26 -

2.2.4.3 tert-butyl ((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylcarbamate

(1R,4R)-4-((tert-butoxycarbonylamino)methyl)cyclohexanecarboxylicacid(300mg, 1.17mmol) DMF 10ml EDC(290mg, 1.52mmol), HOBT(236mg, 1.75mmol) 1 . 2,2-Diphenylethylamine(230mg, 1.17mmol) TEA(488, 3.5mmol) 24 . TLC EA MgSO4 . MeOH MC (1:8) flesh column chromatography tert-butyl((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylcarbamate(420mg, 0.962mmol) .

Yield : 83% Rf : 0.61 (MeOH:MC=1:8)1

H-NMR (CDCl3, 400MHz) : 7.27~7.30 (4H, m), 7.18~7.21 (6H, m), 5.36 (1H, s), 4.16 (1H, t, J=8Hz), 3.85 (2H, t, J=6Hz), 2.91 (2H, t,

J=6.4Hz), 1.82~1.88 (1H, m), 1.71~1.75 (4H, m), 1.39 (9H, s),1.30~1.36 (3H, m), 0.83~0.89 (2H, m)13

C-NMR (CDCl3, 100MHz) : 175.48, 155.90, 141.70, 128.59, 127.94, 126.71, 79.20, 50.54, 46.54, 45.37, 43.57, 37.69, 29.77, 28.93, 28.45

- 27 -

2.2.4.4 (1R,4R)-4-(aminomethyl)-N-(2,2-diphenylethyl)cyclohexanecarboxamide

tert-butyl ((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylcarbamate(350mg, 0.801mmol) MC 8ml , 0 TFA 2ml 2 . TLC TFA salt (1R,4R)-4-(aminomethyl)-N-(2,2-diphenylethyl)cyclohexanecarboxamide(540mg, 1.20mmol) .

Yield : crude Rf : 0.36 (MeOH:MC=1:8)1

H-NMR (CDCl3, 400MHz) : 7.24~7.32 (4H, m), 7.19~7.23 (6H, m), 6.23 (1H, s), 4.16 (1H, t, J=8Hz), 3.91 (2H, t, J=6Hz), 2.90 (2H, t,

J=6.4Hz), 2.09 (1H, m), 1.75~1.81 (4H, m), 1.56 (2H, m), 1.25~1.33(4H, m), 0.93~0.96 (2H, m)13

C-NMR

(CDCl3,

100MHz)

:

178.32,

140.61,

128.83,

127.77,

127.19, 50.06, 46.55, 44.49, 44.15, 34.77, 28.51, 27.82

2.2.4.5 methyl 4-(((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylamino)-4-oxobutanoate

- 28 -

mono-Methyl succinate(106mg, 0.801mmol) TEA(123, 0.883mmol) MC 3ml , 0 MC pivaloyl chloride (99, 0.801mmol) dropwise 0 1 . 1 0 TEA(370, 2.65mmol) MC 7ml (1R,4R)-4-(aminomet hyl)-N-(2,2-diphenylethyl)cyclehexanecarboxamide(361mg, 0.801mmol) 24 . TLC MC 30% citric acid, brine, saturated NaHCO3(aq) , MgSO4 . MeOH MC (1:8) flesh column chromatography methyl 4-(((1R,4R)-4(2,2-diphenylethylcarbamoyl)cyclohexyl)methylamino)-4-oxobutanoate(28 0mg, 0.621mmol) .19)

Yield : 78% Rf : 0.52 (MeOH:MC=1:8)1

H-NMR (CDCl3, 400MHz) : 7.27~7.32 (4H, m), 7.20~7.24 (6H, m), 5.85 (1H, s), 5.44 (1H, s), 4.18 (1H, t, J=8Hz), 3.86 (2H, t, J=6Hz), 3.67 (3H, s), 3.06 (2H, t, J=6.4Hz), 2.65 (2H, t, J=6.4Hz), 2.45 (2H, t,

J=6.4Hz), 1.86~1.87 (1H, m), 1.73~1.77 (4H, m), 1.41~1.23 (3H, m),0.86~0.90 (2H, m)13

C-NMR (CDCl3, 100MHz) : 175.45, 173.34, 171.24, 141.67, 128.57, 127.82, 126.70, 51.86, 50.51, 45.41, 45.27, 43.56, 37.34, 31.07, 29.82, 29.44, 28.89

- 29 -

2.2.4.6 4-(((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylamino)-4-oxobutanoic acid

methyl

4-(((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methyla-

mino)-4-oxobutanoate(265mg, 0.588mmol) 30% MeOH 20ml , LiOH(29mg, 1.18mmol) 5 . TLC MC starting . 10% HCl(aq) pH3 . MC MgSO4 . MeOH MC (1:8) flesh column chromatography 4-(((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylamino)-4-oxobutanoic acid(217mg, 0.497mmol) .19)

Yield : 85% Rf : 0.32 (MeOH:MC=1:8)1

H-NMR (CD3OD, 400MHz) : 7.15~7.27 (10H, m), 4.25 (1H, t, J=8.4Hz), 3.76 (2H, t, J=6Hz), 2.96 (2H, t, J=6.4Hz), 2.56 (2H, t,

J=6.8Hz), 2.43 (2H, t, J=6.8Hz), 1.96~1.98 (1H, m), 1.73~1.76 (2H,m), 1.58~1.61 (2H, m), 1.30~1.39 (3H, m), 0.86~0.91 (2H, m)13

C-NMR (CD3OD, 100MHz) : 178.75, 176.00, 174.30, 143.62, 129.38, 129.05, 127.47, 51.73, 46.48, 46.19, 44.77, 38.64, 31.56, 30.93, 30.36, 30.10

- 30 -

2.2.4.7 (1R,4R)-N-(2,2-diphenylethyl)-4-((4-((S)-2-(hydroxymethyl)pyrrolidin-1-yl)-4-oxobutanamido)methyl)cyclohexanecarboxamide

4-(((1R,4R)-4-(2,2-diphenylethylcarbamoyl)cyclohexyl)methylamino)-4oxobutanoic acid(100mg, 0.229mmol) TEA(36, 0.252mmol) MC 3ml , 0 MC pivaloyl chloride (29, 0.229mmol) dropwise 0 1 . MC 1ml L-prolinol(25, 0.252mmol) TEA(36, 0.252mmol) 0 dropwise 24 . TLC MC 30% citric acid, brine, saturated NaHCO3(aq) MgSO4 . MeOH MC (1:8) flesh column chromatography (1R,4R)-N-(2,2-diphenylethyl)-4-((4-((S)-2-(hydroxymethyl)pyrrolidin-1-yl)-4-oxobutanamido)metyl)cyclohexanecarboxamide(73mg, 0.140mmol) .19)

Yield : 85% Rf : 0.37 (MeOH:MC=1:8)1

H-NMR (CDCl3, 400MHz) : 7.28~7.31 (4H, m), 7.19~7.23 (6H, m), 6.34 (1H, s), 5.66 (1H, s), 5.00 (1H, s), 4.18 (1H, t, J=8Hz), 3.85 (2H, t, J=6Hz), 3.46~3.60 (5H, m), 3.08~3.13 (1H, m), 2.99~3.03 (1H, m), 2.63 (2H, t, J=6.4Hz), 2.49 (2H, t, J=6.8Hz), 2.04 (1H, s), 1.83~2.02 (4H, m), 1.71~1.74 (4H, m), 1.26~1.42 (3H, m), 0.85~0.92 (2H, m)

13

C-NMR (CDCl3, 100MHz) : 175.70, 172.82, 172.19, 141.75, 128.52,

- 31 -

127.92, 126.61, 66.55, 61.24, 50.48, 48.04, 45.20, 43.56, 37.25, 31.23, 30.57, 29.68, 29.64, 28.96, 28.22, 24.29

2.2.4.8 (1R,4R)-N-(2,2-diphenylethyl)-4-((4-((S)-2-formylpyrrolidin-1-yl)-4-oxobutanamido)methyl)cyclohexanecarboxamide

(1R,4R)-N-(2,2-diphenylethyl)-4-((4-((S)-2-(hydroxymethyl)pyrrolidin1 -y l ) -4 -o xobu ta na mi do) m ethyl ) c yc l ohexa n eca rbo xa mi de( 6 0 mg, 0.115mmol) TEA(48, 0.346mmol) DMSO anhydrous 1.5ml , DMSO anhydrous 1.5ml SO3 pyridine complex(55mg, 0.346mmol) , 2 . TLC reaction mixture ice water 20ml chloroform . chloroform 30% citric acid, brine, saturated NaHCO3(aq) MgSO4 . MeOH chlorof -orm (1:10) flesh column chromatography

(1R,4R)-N-(2,2-diphenylethyl)-4-((4-((S)-2-formylpyrrolidin-1-yl)-4-oxobutanamido)methyl)cyclohexanecarboxamide(25mg, 0.048mmol) .19)

Yield : 42% Rf : 0.43 (MeOH:MC=1:8)1

H-NMR

(CDCl3,

600MHz) :

9.41 (1H, s),

7.28~7.31 (4H, m),

7.20~7.23 (6H, m), 6.30 (1H, s), 5.61 (1H, s), 4.37 (1H, m), 4.18 (1H, t, J=8Hz), 3.83~3.90 (2H, m), 3.60~3.63 (1H, m), 3.55~3.58 (1H, m)

- 32 -

3.08~3.13 (1H, m), 2.98~3.02 (1H, m), 2.64~2.70 (2H, m), 2.50~2.52 (2H, m), 2.03~2.10 (1H, m), 1.93~2.03 (3H, m), 1.83~1.88 (2H, m), 1.72~1.74 (4H, m), 1.30~1.42 (3H, m), 0.84~0.92 (2H, m)13

C-NMR (CDCl3, 150MHz) : 199.02, 175.75, 172.23, 171.42, 141.86, 128.64, 128.03, 126.74, 64.96, 50.50, 47.11, 45.25, 43.53, 37.22, 31.10, 29.98, 29.66, 28.92, 27.60 25.99, 24.88

- 33 -

2.2.4.9 R3 derivatives R3 derivatives .

O H N O N H OH Oa

O H N O N H N O O OMe

reagents and condition : (a) L-proline methyl ester, EDC, HOBT, TEA, DMF

O H N O N H OH O

a b c d

O H N O N H N O O NH2

reagents and condition : (a) L-proline, NaHCO3, (Boc)2O, MeOH; (b) (S)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid, TEA, Ethyl chloroformate, 30% NH3 solution, THF21); (c) (S)-tert-butyl 2-carbamoylpyrrolidine-1-carboxylate, TFA, MC; (d) (S)-pyrrolidine-2-carboxamide, EDC, HOBT, TEA, DMF

O H N O N H OH O

a b c d e

O H N O N H N O CN

reagents and condition : (a) L-proline, NaHCO3, (Boc)2O, MeOH; (b) (S)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid, TEA, Ethyl chloroformate, 30% NH3 solution, THF17); (c)21)

(S)-tert-butyl

2-carbamoylpyrrolidine-1-carboxylate,

TEA,

TFAA,

THF

anhydrous

; (d) (S)-tert-butyl 2-cyanopyrrolidine-1-carboxylate, TFA, MC; (e) (S)-py-

rrolidine-2-carbonitrile, EDC, HOBT, TEA, DMF

- 34 -

2.2.5 Enzyme assay

NO2 O O O H N N O N H

NH2

PEP

NO2

Z-G ly-Pro-PNA (317nm)

p-nitroaniline (380nm)

Fig. 8. UV-Vis

PEP(Prolyl endopeptidase) inhibitory activity Toda .22) 50Unit PEP 0.1M phosphate buffer (pH 7.0) 0.1Unit . Buffer sodium phosphate mono basic 0.1M sodium phosphate dibasic 0.1M pH 7.0 . Substrate Z-Gly-Pro-pNA(C21H22N4O6 : 426) 10mg 40% dioxane 11.7 2mM . Substrate Z-Gly-Pro-pNA 317nm PEP amide bond pNA 380nm . PEP inhibitory activity UV-Vis spectrophotometer 380nm , 37 2 30 time scanning. Enzyme 0.008Unit, substrate 0.16mM , Enzyme, substrate, sample, buffer 1ml(1000) . Sample MeOH solvent , MeOH sample buffer . Solvent inhibition sample MeOH 0.4% 4% . inhibition percentage table 3. .15,24)

- 35 -

0.1M Phosphate buffer (pH 7.0 / 800 / 37)

A

2mM Z-Gly-Pro-pNA 80 Sample 40 0.1U PEP 80 (380nm) 0.1M Phosphate buffer

B

(pH 7.0 / 960) Sample 40

0.1M Phosphate buffer (pH 7.0 / 800 / 37)

Control

2mM Z-Gly-Pro-pNA 80 Solvent 40 0.1U PEP 80 (380nm)

0.1M Phosphate buffer (pH 7.0 / 800 / 37)

Positive control

2mM Z-Gly-Pro-pNA 80 Z-Pro-prolinal 40 0.1U PEP 80 (380nm)

Inhibition %

A380 Of Control - (A-B) A380 Of Control

x 100

Table 3. Method of PEP assay

- 36 -

3. PEP inhibitor PEP inhibitory activity .

Dipeptide bond succinamide R1, R2, R3 group . R1, R2, R3 group 6, 27, 5 38 PEP inhibitors .

3.1 PEP inhibitor synthesis R1 R1 group inhibitor P2 position P3 position linker . R1 group P2 position succinamide , S1 pocket R3 group pyrrolidine . phenyl group 3-aminobenzoic acid, 4-aminobenzoic acid, 4(aminomethyl)benzoic acid , aromatic amino acid cyclohexane piperazine cis-4-aminocyclohexanecar-

boxylic acid, trans-4-(aminomethyl)cyclohexanecarboxylic acid, ethyl piperazino acetate , 6 amino acid PEP activity . PEP assay ethyl piperazino acetate trans-4-(aminomethyl)cyclohexanecarboxylic acid, 4-(aminomethyl)benzoic acid . 3 amino acid activity aromatic amino acid trans-4-(aminomethyl)cyclohexanecarboxylic acid R1 group . R2 R2 group R1 group pyrrolidine, succinamide , R1 group trans-4-(amino-

- 37 -

methyl)cyclohexanecarboxylic acid . S3 pocket R2 group aromatic, cycloalkyl, aliphatic, piperazine 27 amine , ring size, chain , S3 pocket hydrophobic interaction . PEP assay 2,2-diphenylethylamine R2 group . S3 pocket hydrophobic interaction , ring size amine . R3 S1 pocket proline specific , PEP enzyme residues Ser554 pocket. pyrrolidine ring pyrrolidine ring 2 reactive functional group catalytic active site interaction inhibitor potency . R3 group succinamide , R1, R2 group trans-4-(aminomethyl)cyclohexanecarboxylic acid, 2,2-diphenylethylamine R3 group inhibitor . R3 group L-proline methyl ester, L-prolinol, L-prolinal, L-prolinamide, 2(S)-cyanopyrrolidine inhibitor , PEP assay Lprolnal 2(S)-cyanopyrrolidine pyrrolidine . L-prolinal 150 . R3 group potency ,

L-prolinal PEP enzyme residue Ser554 hydroxy group hemiacetal adduct .15)

- 38 -

3.2 Enzyme assay 38 compound PEP assay table 4. . PEP (8ppm 10%) - .

Name

Structure

Scheme

IC50(M)

PEP-01

1

6.43

PEP-02

1

8.55

PEP-03

1

11.30

PEP-04

1

26.50

PEP-05

1

-

PEP-06

1

-

- 39 -

PEP-07

2

9.31

PEP-08

2

27.50

PEP-09

2

28.02

PEP-10

2

24.10

PEP-11

2

24.30

PEP-12

2

23.50

PEP-13

2

19.02

- 40 -

PEP-14

2

7.06

PEP-15

2

16.99

PEP-16

2

30.61

PEP-17

2

36.60

PEP-18

2

47.44

PEP-19

2

5.28

PEP-20

2

19.47

- 41 -

PEP-21

2

19.01

PEP-22

2

19.17

PEP-23

2

15.15

PEP-24

2

31.97

PEP-25

2

11.63

PEP-26

2

16.85

PEP-27

2

8.40

- 42 -

PEP-28

2

15.05

PEP-29

2

17.46

PEP-30

2

11.93

PEP-31

2

12.08

PEP-32

2

14.56

PEP-33

2

0.91

PEP-34

3

0.17

- 43 -

PEP-35

3

-

PEP-36

3

0.00641

PEP-37

3

-

PEP-38

3

-

Table 4. PEP inhibitory activity of synthesized compounds

- 44 -

4.

PEP inhibitor .

inhibitor PEP enzyme dipeptide bond , flexible succinamide 38 inhibitors , S1, S2, S3 pocket computer docking . computer , computer PEP inhibitor . PEP assay (PEP-36) IC50=6.41nM PEP , .

Chemical structure of PEP-36

- 45 -

5. 1. Brandts, J. F.; Halvorson, H. R.; Brennan, M. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 1975, 14, 4953-4963. 2. Vanhoof, G.; Goossens, F.; De Meester, I.; Hendriks, D.; Scharpe, S. Proline motifs in peptides and their biological processing. FASEB J. 1995, 9, 736-744. 3. Yaron, A.; Naider, F. Proline-dependent structural and biological properties of peptides and proteins. Crit. Rev. Biochem. Mol. Biol. 1993, 28, 31-81. 4. Walter, R., Shlank, H., Glass, J. D., Schwartz, I. L. and Kerenyi, T. D. (1971) Leucylglycinamide released from oxytocin by human uterine enzyme. Science 173, 827-829. 5. Venalainen, J. I., Juvonen, R. O. and Mannisto, P. T. (2004) Evolutionary relationships of the prolyl oligopeptidase family

enzymes. Eur. J. Biochem. 271, 2705-2715. 6. Kato, T., Okada, M. and Nagatsu, T. (1980) Distribution of post-proline cleaving enzyme in human brain and the peripheral tissues. Mol. Cell. Biochem. 32, 117-121 7. Yoshimoto, T., Ogita, K., Walter, R., Koida, M. and Tsuru, D. (1979) Post-proline cleaving enzyme: synthesis of a new fluorogenic

substrate and distribution of the endopeptidase in rat tissues and body fluids of man. Biochem. Biophys. Acta 569, 184-192. 8. Irazusta, J., Larrinaga, G., Gonalez-Maeso, J., Gil, J., Meana, J. J. and Casis, L. (2002) Distribution of prolyl endopeptidase activities in rat and human brain. Neurochem. Int. 40, 337-345. 9. Kowall, N. W., Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7247-7251

- 46 -

10. Koida, M.; Walter, R. Post-proline cleaving enzyme. Purification of this endopeptidase by affinity chromatography. J. Biol. Chem. 1976,

251, 7593-7599.11. Walter, R. Partial purification and characterization of postproline cleaving hormones enzyme: by enzymatic inactivation of of neurohypophyseal species. Biochim.

kidney preparations

various

Biophys. Acta 1976, 422, 138-158. 12. Wilk, S. Prolyl endopeptidase. Life Sci. 1983, 33, 2149-2157. 13. Janice Lawandi, Sandrin Gerber-Lemaire, Lucienne Juillerat-Jeannere -t, and Nicolas Moitessier. Inhibitor of prolyl oligopeptidases for the theraph of human diseases: Defining diseases and inhibitors J. Med. Chem., 2010, 53(9), 3423-3438 14. Han, H.-G. (2009) Design synthesis and QSAR study of pyrrolidine containing amides and 2-alkylamidobenzoic acid derivatives as PEP inhibitors Kyung Hee Univ. Thesis, 40-41 15. Fulop, V., Bocskei, Z. and Polgar, L. (1998), Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. Cell 94, 161-170. 16. Shan, L.; Mathews, I. I.; Khosla, C. Structural and mechanistic analysis of two prolyl endopeptidases: role of interdomain dynamics in catalysis and specificity. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 3599-3604. 17. Saito, M.; Hashimoto, M.; Kawaguchi, N.; Fukami, H.; Tanaka, T.; Higuchi, N. Synthesis and inhibitory activity of acyl-peptidylprolinal derivatives toward post-proline cleaving enzyme as nootropic

agents. J. Enzyme Inhib. 1990, 3, 163178. 18. Saito, M.; Hashimoto, M.; Kawaguchi, N.; Shibata, H.; Fukami, H.; Tanaka, T.; Higuchi, N. Synthesis and inhibitory activity of

acyl-peptidyl-pyrrolidine derivatives toward post-proline cleaving enzyme; a study of subsite specificity. J. Enzyme Inhib. 1991, 5,

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5175. 19. Erik A. A. Wallen, Johannes A. M. Christiaans, Markus M. Forsberg, Jarkko I. Vena lainen, Pekka T. Mannisto, Jukka Gynther,. Dicarboxylic Acid bis(L-prolyl-pyrrolidine)Amides as Prolyl

Oligopeptidase Inhibitors. J. Med. Chem. 2002, 45, 4581-4584 20. Jiabo Li and Yaowu Sha. A convenient Synthesis of Amino Acid Methyl Ester. Molecules 2008, 13, 1111-1119 21. Tang, F.-Y.; Qu, L.-Q.; Xu, Y.; Ma, R.; Chen, S. H and Li, G. Preparation of a-azaspiro-bicyclo templates, application no.

200610027069.9, May 30, 2006. 22. Soichiro Toda, Yumiko Obi, Kei-ichi Numata, Yasutaro Hamagishi, Koji Tomita, Nobujiro Komiyama, Chikako Kotake, Tamotsu Furumai and Toshikazu Oki. (1992) Eurystatins A And B, New Prolyl endopepidase inhibitors J. Antibiotics. 45, 1573-1579 24. Park, Y.-S., (2006) Search for anti-amnestic constituents from natural resources, 8-9

- 48 -

6.

Fig. 9. 1H-NMR spectrum of (PEP-33)

Fig. 10.

13

C-NMR spectrum of (PEP-33)

- 49 -

Fig. 11. 1H-NMR spectrum of (PEP-36)

Fig. 12.

13

C-NMR spectrum of (PEP-36)

- 50 -

Abstract

Synthesis of Succinamide Backbone Derivatives as Prolyl Endopeptidase Inhibitors.Yoon Seung-Bin Department of Chemistry Graduate School Kyung Hee University

Among the 20 common amino acids, proline has a unique role because of its cyclic structure. It may serve as a regulatory structure in maturation and degradation of peptides and in protein folding. Prolyl endopeptidase (PEP; E.C. 3.4.21.26) is a proline-specific serine peptidase that

preferentially hydrolyzes peptides at the carboxyl side of proline. In vitro Studies have shown that PEP cleaves a number of proline-containing neuropeptides which a related to the processes of learning and memory. Compounds with PEP inhibitory activity are expected to prevent memory loss and neurodegenerative diseases of the central nervous system. In this research, PEP inhibitors with various kind of carbon skeletons were predicted by using the docking tool in the Discovery studio 2.0 program and we synthesized 38 compounds containing succinamide backbone and measured their IC50 values on PEP inhibition. Among them PEP-36 showed the most potent PEP inhibitor activity with an IC50 value of 6.41nM.

- 51 -

Synthesis of Succinamide Backbone Derivatives as Prolyl Endopeptidase Inhibitors.Yoon Seung-Bin Department of Chemistry Graduate School Kyung Hee University

20 amino acid cyclic structure proline peptidase peptide peptide protein folding peptide .1~3) Prolyl endopeptidase (PEP, EC 3.4.21.26) proline carboxyl side peptide proline-specific serine peptidase 1971 walter4) oxytocin-cleaving enzyme , .5~7)

PEP , , , ,

, .8) PEP vasopressin, substance P, thyrotropin-releasing hormone(TRH) proline neuropeptide 9), vasopressin , substance P

amyloid neurotoxicity . cognition- enhancing neuropeptides PEP substrates PEP .10~12) Discovery studio 2.0 docking , succinamide 38 inhibitor . compound PEP inhibitory activity . 38

- 52 -

compound 8ppm 10% compound 33 compound 47.44M~0.0064M , (PEP-36) IC50=6.41nM PEP inhibitory activity .

- 53 -