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Chemical Structure| 138112-76-2 Chemical Structure| 138112-76-2
Chemical Structure| 138112-76-2

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Agomelatine

CAS No.: 138112-76-2

Agomelatine is a melatonin structurely similar 5-HT2C receptor antagonist as well as a potent melatonin receptor agonist, used to treat major depressive disorder.

Synonyms: S-20098

4.5 *For Research Use Only !

Cat. No.: A643275 Purity: 98%

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Product Details of [ 138112-76-2 ]

CAS No. :138112-76-2
Formula : C15H17NO2
M.W : 243.30
SMILES Code : CC(NCCC1=C2C=C(OC)C=CC2=CC=C1)=O
Synonyms :
S-20098
MDL No. :MFCD00916659
InChI Key :YJYPHIXNFHFHND-UHFFFAOYSA-N
Pubchem ID :82148

Safety of [ 138112-76-2 ]

GHS Pictogram:
Signal Word:Warning
Hazard Statements:H302-H315-H319-H335
Precautionary Statements:P261-P305+P351+P338

Calculated chemistry of [ 138112-76-2 ] Show Less

Physicochemical Properties

Num. heavy atoms 18
Num. arom. heavy atoms 10
Fraction Csp3 0.27
Num. rotatable bonds 5
Num. H-bond acceptors 2.0
Num. H-bond donors 1.0
Molar Refractivity 72.83
TPSA ?

Topological Polar Surface Area: Calculated from
Ertl P. et al. 2000 J. Med. Chem.

38.33 Ų

Lipophilicity

Log Po/w (iLOGP)?

iLOGP: in-house physics-based method implemented from
Daina A et al. 2014 J. Chem. Inf. Model.

2.6
Log Po/w (XLOGP3)?

XLOGP3: Atomistic and knowledge-based method calculated by
XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry

2.72
Log Po/w (WLOGP)?

WLOGP: Atomistic method implemented from
Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.

2.53
Log Po/w (MLOGP)?

MLOGP: Topological method implemented from
Moriguchi I. et al. 1992 Chem. Pharm. Bull.
Moriguchi I. et al. 1994 Chem. Pharm. Bull.
Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.

2.42
Log Po/w (SILICOS-IT)?

SILICOS-IT: Hybrid fragmental/topological method calculated by
FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com

3.28
Consensus Log Po/w?

Consensus Log Po/w: Average of all five predictions

2.71

Water Solubility

Log S (ESOL):?

ESOL: Topological method implemented from
Delaney JS. 2004 J. Chem. Inf. Model.

-3.14
Solubility 0.175 mg/ml ; 0.000719 mol/l
Class?

Solubility class: Log S scale
Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly

Soluble
Log S (Ali)?

Ali: Topological method implemented from
Ali J. et al. 2012 J. Chem. Inf. Model.

-3.18
Solubility 0.161 mg/ml ; 0.000663 mol/l
Class?

Solubility class: Log S scale
Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly

Soluble
Log S (SILICOS-IT)?

SILICOS-IT: Fragmental method calculated by
FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com

-5.4
Solubility 0.00096 mg/ml ; 0.00000394 mol/l
Class?

Solubility class: Log S scale
Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly

Moderately soluble

Pharmacokinetics

GI absorption?

Gatrointestinal absorption: according to the white of the BOILED-Egg

High
BBB permeant?

BBB permeation: according to the yolk of the BOILED-Egg

Yes
P-gp substrate?

P-glycoprotein substrate: SVM model built on 1033 molecules (training set)
and tested on 415 molecules (test set)
10-fold CV: ACC=0.72 / AUC=0.77
External: ACC=0.88 / AUC=0.94

No
CYP1A2 inhibitor?

Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set)
and tested on 3000 molecules (test set)
10-fold CV: ACC=0.83 / AUC=0.90
External: ACC=0.84 / AUC=0.91

Yes
CYP2C19 inhibitor?

Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set)
and tested on 3000 molecules (test set)
10-fold CV: ACC=0.80 / AUC=0.86
External: ACC=0.80 / AUC=0.87

Yes
CYP2C9 inhibitor?

Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set)
and tested on 2075 molecules (test set)
10-fold CV: ACC=0.78 / AUC=0.85
External: ACC=0.71 / AUC=0.81

No
CYP2D6 inhibitor?

Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set)
and tested on 1068 molecules (test set)
10-fold CV: ACC=0.79 / AUC=0.85
External: ACC=0.81 / AUC=0.87

Yes
CYP3A4 inhibitor?

Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set)
and tested on 2579 molecules (test set)
10-fold CV: ACC=0.77 / AUC=0.85
External: ACC=0.78 / AUC=0.86

No
Log Kp (skin permeation)?

Skin permeation: QSPR model implemented from
Potts RO and Guy RH. 1992 Pharm. Res.

-5.85 cm/s

Druglikeness

Lipinski?

Lipinski (Pfizer) filter: implemented from
Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev.
MW ≤ 500
MLOGP ≤ 4.15
N or O ≤ 10
NH or OH ≤ 5

0.0
Ghose?

Ghose filter: implemented from
Ghose AK. et al. 1999 J. Comb. Chem.
160 ≤ MW ≤ 480
-0.4 ≤ WLOGP ≤ 5.6
40 ≤ MR ≤ 130
20 ≤ atoms ≤ 70

None
Veber?

Veber (GSK) filter: implemented from
Veber DF. et al. 2002 J. Med. Chem.
Rotatable bonds ≤ 10
TPSA ≤ 140

0.0
Egan?

Egan (Pharmacia) filter: implemented from
Egan WJ. et al. 2000 J. Med. Chem.
WLOGP ≤ 5.88
TPSA ≤ 131.6

0.0
Muegge?

Muegge (Bayer) filter: implemented from
Muegge I. et al. 2001 J. Med. Chem.
200 ≤ MW ≤ 600
-2 ≤ XLOGP ≤ 5
TPSA ≤ 150
Num. rings ≤ 7
Num. carbon > 4
Num. heteroatoms > 1
Num. rotatable bonds ≤ 15
H-bond acc. ≤ 10
H-bond don. ≤ 5

0.0
Bioavailability Score?

Abbott Bioavailability Score: Probability of F > 10% in rat
implemented from
Martin YC. 2005 J. Med. Chem.

0.55

Medicinal Chemistry

PAINS?

Pan Assay Interference Structures: implemented from
Baell JB. & Holloway GA. 2010 J. Med. Chem.

0.0 alert
Brenk?

Structural Alert: implemented from
Brenk R. et al. 2008 ChemMedChem

0.0 alert: heavy_metal
Leadlikeness?

Leadlikeness: implemented from
Teague SJ. 1999 Angew. Chem. Int. Ed.
250 ≤ MW ≤ 350
XLOGP ≤ 3.5
Num. rotatable bonds ≤ 7

No; 1 violation:MW<1.0
Synthetic accessibility?

Synthetic accessibility score: from 1 (very easy) to 10 (very difficult)
based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties,
trained on 12'782'590 molecules and tested on 40 external molecules (r2 = 0.94)

1.4

Application In Synthesis [ 138112-76-2 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

  • Downstream synthetic route of [ 138112-76-2 ]

[ 138112-76-2 ] Synthesis Path-Downstream   1~2

  • 2
  • [ 108-24-7 ]
  • [ 138113-08-3 ]
  • [ 138112-76-2 ]
YieldReaction ConditionsOperation in experiment
89% With hydrogen;Raney nickel; In ethanol; water; at 70℃; under 22502.3 Torr; Step C: N-[2-(7-Methoxy-1-naphthyl)ethyl]acetamide There are introduced into an 8 litre reactor 136 g of Raney nickel, 2.06 litres of ethanol and 0.23 litre of water. Whilst stirring at 70 C. and under 30 bars of hydrogen, the compound obtained in Step B (0.8 kg), dissolved in acetic anhydride (2.4 litres), is added slowly. At the end of the addition, the reaction mixture is stirred for 1 hour under hydrogen at 30 bars; the reactor is then subjected to decompression and the liquors are filtered. After concentrating the mixture, the residue is crystallized from an ethanol/water 35/65 mixture to yield the title product in a yield of 89% and with a chemical purity of more than 99%. Melting point: 108 C.
89% With hydrogen; In ethanol; water; at 70℃; under 22502.3 Torr; The reaction was carried out on a larger batch in order to optimise the yield obtained: 136 g of Raney nickel, 2.06 L of ethanol and 0.23 L of water are introduced into an 8 L reactor. Whilst stirring at 70 C. and under 30 bars of hydrogen, the compound obtained in Step D (0.8 kg) dissolved in acetic anhydride (2.4 L) is slowly added. At the end of the addition, the reaction mixture is stirred for 1 hour under hydrogen at 30 bar, the reactor is then decompressed and the liquors are filtered. After concentration of the mixture, the residue is crystallised from a mixture of ethanol/water 35/65 to yield the title product in a yield of 89% and with a chemical purity greater than 99%. Melting point: 108 C.
89% With hydrogen; In ethanol; water; at 70℃; under 22502.3 Torr; for 1h; 136 g of Raney nickel, 2.06 L of ethanol and 0.23 L of water are introduced into an 8-L reactot Whilst stirring at 70 C. and under 30 bars of hydrogen, the compound obtained in Step D above (0.8 kg) dissolved in acetic anhydride (2.4 L) is added slowly. When the addition is complete, the reaction mixture is stirred for 1 hour under hydrogen at 30 bars, and then the reactor is depressurised and the liquors are filtered. Afier concentration of the mixture, the residue is crystallised from a mixture of ethanol/water 35/65 to yield the title product in a yield of 89% and with a chemical purity greater than 99%.10075] Melting point: 108 C. ?H NMR spectroscopic analysis (CD3OD, 300.13MHz, oe in ppm): 8.21 (bs, 1H); 7.74 (d, J=8.9 Hz, 1H); 7.65 (d, J=8.0 Hz, 1H); 7.52 (d, J=2.5 Hz, 1H); 7.31-7.2 (m, 2H); 7.11 (dd, J=8.9 and 2.5 Hz, 1H); 3.96 (s, 3H); 3.52-3.44 (m, 2H); 3.23-3.18 (m, 2H); 1.94 (s, 3H). ?3C NMR spectroscopic analysis (CD3OD, 75.5 MHz, oe in ppm): 173.4 (s); 159.4 (s); 135.1 (s); 134.6 (s); 131.2 (d); 130.8 (s); 128.2 (d); 127.9 (d); 124.2 (d); 119.3 (d); 103.2 (d); 55.9 (q); 41.4 (0; 34.2 (0; 22.6 (q).
In 10L reactor 2-(7-methoxynaphthalen-1 -yl)acetonitrile (750g), methanol (6,3L), NaOH solution (228g NaOH is diluted in 750ml_ water) and 134g of Raney-Nickel is charged. Reaction mixture is stired at 30C and 4 bar H2 and monitored with HPLC. After reaction is done, it is cooled to 15C and acetic anhydride (750mL) is added and warmed to 25C. Reaction is monitored with HPLC. Once the reaction is finished it is filtered, solvent evaporated, than ethyl acetate (5L) is added and organic phase is extracted with water (5L). Solvent is evaporated to obtain agomelatine of 96,4% HPLC purity.

 

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