Structure of 166815-96-9
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Berg, Kaja ; Hegde, Pooja ; Pujari, Venugopal ; Brinkmann, Marzena ; Wilkins, David Z. ; Parish, Tanya , et al.
Abstract: The electron transport chain (ETC) in the cell membrane consists of a series of redox complexes that transfer electrons from electron donors to acceptors and couples this electron transfer with the transfer of protons (H+) across a membrane. This process generates proton motive force which is used to produce ATP and a myriad of other functions and is essential for the long-term survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis (TB), under the hypoxic conditions present within infected granulomas. Menaquinone (MK), an important carrier molecule within the mycobacterial ETC, is synthesized de novo by a cluster of enzymes known as the classic/canonical MK biosynthetic pathway. MenA (1,4-dihydroxy-2-naphthoate prenyltransferase), the antepenultimate enzyme in this pathway, is a verified target for TB therapy. In this study, we explored structure-activity relationships of a previously discovered MenA inhibitor scaffold, seeking to improve potency and drug disposition properties. Focusing our campaign upon three molecular regions, we identified two novel inhibitors with potent activity against MenA and Mtb (IC50 = 13-22 μM, GIC50 = 8-10 μM). These analogs also displayed substantially improved pharmacokinetic parameters and potent synergy with other ETC-targeting agents, achieving nearly complete sterilization of Mtb in combination therapy within two weeks in vivo. These new inhibitors of MK biosynthesis present a promising new strategy to curb the continued spread of TB.
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Keywords: 1,4-dihydroxy-2-naphthoate prenyltransferase ; MenA ; MenA inhibitors ; Menaquinone ; Mtb ; Mycobacterium tuberculosis ; Piperidine derivatives ; SAR
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Purchased from AmBeed: 25952-53-8 ; 90719-32-7 ; 872-85-5 ; 6457-49-4 ; 3769-41-3 ; 10338-57-5 ; 135-19-3 ; 135-19-3 ; 28177-48-2 ; 22246-18-0 ; 122334-37-6 ; 91914-06-6 ; 10040-98-9 ; 161975-39-9 ; 150-76-5 ; 371-41-5 ; 63754-96-1 ; 288-32-4 ; 3380-34-5 ; 1677-46-9 ; 166815-96-9 ; 700-57-2 ; 1204-86-0 ; 21725-69-9 ; 367-12-4 ; 1003-29-8 ; 627-35-0 ; 27292-49-5 ; 104324-16-5 ; 123855-51-6 ; 180847-23-8 ; 4328-13-6 ; 875401-70-0 ; 405272-71-1 ; 63614-86-8 ; 1420942-13-7 ; 25952-53-8 ; 1420895-21-1 ; 1078-18-8 ; 32363-45-4 ; 69564-68-7 ; 31519-22-9 ; 22246-18-0 ; 189618-33-5 ; 180847-24-9 ; 6264-98-8 ; 946680-75-7 ; 63608-38-8 ; 713-68-8 ; 62810-39-3 ; 189618-32-4 ; 63608-31-1 ; 15789-05-6 ; 63712-27-6 ; 63608-33-3 ; 63608-35-5
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CAS No. : | 166815-96-9 |
Formula : | C18H27NO5S |
M.W : | 369.48 |
SMILES Code : | C(=O)(OC(C)(C)C)N1CCC(CC1)CO[S](=O)(=O)C2=CC=C(C=C2)C |
MDL No. : | MFCD05864740 |
InChI Key : | DARTVAOOTJKHQW-UHFFFAOYSA-N |
Pubchem ID : | 10642851 |
GHS Pictogram: |
![]() |
Signal Word: | Warning |
Hazard Statements: | H302-H315-H319-H332-H335 |
Precautionary Statements: | P261-P280-P305+P351+P338 |
Num. heavy atoms | 25 |
Num. arom. heavy atoms | 6 |
Fraction Csp3 | 0.61 |
Num. rotatable bonds | 7 |
Num. H-bond acceptors | 5.0 |
Num. H-bond donors | 0.0 |
Molar Refractivity | 100.07 |
TPSA ? Topological Polar Surface Area: Calculated from |
81.29 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
3.82 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
3.2 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
4.05 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
2.74 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
2.09 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
3.18 |
Log S (ESOL):? ESOL: Topological method implemented from |
-3.86 |
Solubility | 0.0507 mg/ml ; 0.000137 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (Ali)? Ali: Topological method implemented from |
-4.58 |
Solubility | 0.00974 mg/ml ; 0.0000264 mol/l |
Class? Solubility class: Log S scale |
Moderately soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-4.2 |
Solubility | 0.0236 mg/ml ; 0.0000638 mol/l |
Class? Solubility class: Log S scale |
Moderately soluble |
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 |
No |
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) |
No |
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) |
Yes |
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
Yes |
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
Yes |
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) |
No |
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) |
No |
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from |
-6.28 cm/s |
Lipinski? Lipinski (Pfizer) filter: implemented from |
0.0 |
Ghose? Ghose filter: implemented from |
None |
Veber? Veber (GSK) filter: implemented from |
0.0 |
Egan? Egan (Pharmacia) filter: implemented from |
0.0 |
Muegge? Muegge (Bayer) filter: implemented from |
0.0 |
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat |
0.55 |
PAINS? Pan Assay Interference Structures: implemented from |
0.0 alert |
Brenk? Structural Alert: implemented from |
1.0 alert: heavy_metal |
Leadlikeness? Leadlikeness: implemented from |
No; 1 violation:MW<1.0 |
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) |
3.24 |
* 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.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
98% | With potassium carbonate; In N,N-dimethyl acetamide; at 80℃; for 4h; | Reference Example 4; 6-{ [(1-tert-Butoxycarbonyl) piperidin-4-yl] methoxy}-4- (3-chloro-2-fluoroanilino)-7- methoxyquinazoline; 4- (3-Chloro-2-fluoroanilino)-6-hydroxy-7-methoxyquinazoline (Reference Example 2,700 mg, 2.19 mmol) was dissolved in DMA (35 ml). Potassium carbonate (1209 mg, 8.76 mmol) and tert-butyl 4- (toluene-4-sulfonyloxymethyl) piperidine-l-carboxylate (prepared as described in Example 1 in WO 9427965; 808 mg, 2.19 mmol) were added, and the mixture was stirred at 80C for 4 hours. The solvent was evaporated, and the residue was partitioned between water (100 ml) and DCM (100 ml). The aqueous layer was extracted with DCM (3x 100 ml) and the extractions combined with the DCM layer. The combined DCM fractions were filtered through a silicone-treated filter paper, and evaporated, giving the product as a brown solid (1290 mg, 98%) ; 1H NMR : 1.20 (m, 2H), 1.39 (s, 9H), 1.82 (m, 2H), 2.03 (br. m, 1H), 2.70-2. 85 (br. m, 2H), 3.93 (s, 3H), 3.95-4. 05 (br. m, 2H), 3.98 (d, 2H), 7.19 (s, 1H), 7.26 (dd, 1H), 7.46 (dd, 1H), 7.50 (dd, 1H), 7.76 (s, 1H), 8.35 (s, 1H), 9.57 (s, 1H); Mass Spectrum : 517. 3, 519.3 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
89% | With potassium carbonate; In N-methyl-acetamide; | d) 4-(4-Methylphenylsulphonyloxymethyl)-1-tert-butyloxycarbonylpiperidine (40 g, 0.11 mol) was added to a suspension of ethyl 3-methoxy-4-hydroxybenzoate (19.6 g, 0.1 mol) and potassium carbonate (28 g, 0.2 mol) in dry dimethylformamide (200 ml) and the reaction was heated at 95 C. for 2.5 hours. The reaction was cooled to ambient temperature, partitioned between water and ethyl acetate/diethyl ether, before the organic layer was washed with water and brine. Solvent evaporation in vacuo afforded a clear oil which crystallized on standing. Washing with isohexane and drying in vacuo yielded ethyl 3-methoxy-4-(1-tert-butyloxycarbonylpiperidin-4-ylmethoxy)benzoate (35 g, 89%) as a white solid: m.p. 81-83 C.: 1H NMR (CDCl3): 7.65 (d, 1H), 7.55 (s, 1H), 6.85 (d, 1H), 4.35 (q, 2H), 4.05-4.25 (s, 2H), 3.95 (s, 3H), 3.9 (d, 2H), 2.75 (t, 2H), 2.00-2.15 (m, 2H), 1.80-1.90 (d, 2H), 1.48 (s, 9H), 1.40 (t, 3H), 1.20-1.35 (m, 2H): MS (+ve ESI): 416 (M+Na)30 : |
89% | With potassium carbonate; In DMF (N,N-dimethyl-formamide); at 95℃; for 2.5h; | 4-(4-Methylphenylsulphonyloxymethyl)-1-tert-butyloxycarbonylpiperidine (40g, 0.11mol) was added to a suspension of ethyl 3-methoxy-4-hydroxybenzoate (19.6g, 0.1mol) and potassium carbonate (28g, 0.2mol) in dry DMF (200ml). After stirring at 95C for 2.5 hours, the mixture was cooled to ambient temperature and partitioned between water and ethyl acetate/ether. The organic layer was washed with water, brine, dried (MgSO4) and the volatiles were removed by evaporation. The resulting oil was crystallized from petroleum ether and the suspension was stored overnight (at 5C). The solid was collected by filtration, washed with petroleum ether and dried under vacuum to give ethyl 3-methoxy-4-(1-tert-butyloxycarbonylpiperidin-4-ylmethoxy)benzoate (35g, 89%). m.p. 81-83C 1H NMR Spectrum: (CDCl3) 1.2-1.35(m, 2H); 1.4(t, 3H); 1.48(s, 9H); 1.8-1.9(d, 2H); 2.0-2.15(m, 2H); 2.75(t, 2H); 3.9(d, 2H); 3.95(s, 3H); 4.05-4.25(br s, 2H); 4.35(q, 2H); 6.85(d, 1H); 7.55(s, 1H); 7.65(d, 1H) MS (ESI): 416 [MNa]+ Elemental analysis Found C 63.4 H 8.0 N 3.5 C21H31NO6 0.3H2O Requires C 63.2 H 8.0 N 3.5% |
89% | With potassium carbonate; In N,N-dimethyl-formamide; at 95℃; for 2.5h; | The starting material was prepared as follows: 1-(tert-Butoxycarbonyl)-4-(4-methylphenylsulphonyloxymethyl)piperidine (40g, 0.11mol), (prepared as described for the starting material in Example 1), was added to a suspension of <strong>[617-05-0]ethyl 4-hydroxy-3-methoxybenzoate</strong> (19.6g, 0.1mol) and potassium carbonate (28g, 0.2mol) in dry DMF (200ml). After stirring at 95C for 2.5 hours, the mixture was cooled to ambient temperature and partitioned between water and ethyl acetate/ether. The organic layer was washed with water, brine, dried (MgSO4) and evaporated. The resulting oil was crystallized from petroleum ether and the suspension was stored overnight at 5C. The solid was collected by filtration, washed with petroleum ether and dried under vacuum to give ethyl 4-(1-(tert-butoxycarbonyl)piperidin-4-ylmethoxy)-3-methoxybenzoate (35g, 89%). m.p. 81-83C MS (ESI): 416 [MNa]+ 1H NMR Spectrum: (CDCl3) 1.2-1.35(m, 2H); 1.4(t, 3H); 1.48(s, 9H); 1.8-1.9(d, 2H); 2.0-2.15(m, 2H); 2.75(t, 2H); 3.9(d, 2H); 3.95(s, 3H); 4.05-4.25(br s, 2H); 4.35(q, 2H); 6.85(d, 1H); 7.55(s, 1H); 7.65(d, 1H) |
With potassium carbonate; In DMF (N,N-dimethyl-formamide); at 95℃; for 2.5h; | The 4-amino-6-methoxy-7-(N-methylpiperidin-4-ylmethoxy)quinazoline used as a starting material was prepared as follows: A solution of di-tert-butyl dicarbonate (41.7 g) in ethyl acetate (75 ml) was added dropwise to a stirred solution of ethyl piperidine-4-carboxylate (30 g) in ethyl acetate (150 ml) which had been cooled to 0 to 5 C. in an ice-bath. The resultant mixture was stirred at ambient temperature for 48 hours. The mixture was poured into water (300 ml). The organic layer was separated, washed in turn with water (200 ml), 0.1N aqueous hydrochloric acid solution (200 ml), a saturated aqueous sodium bicarbonate solution (200 ml) and brine (200 ml), dried over magnesium sulphate and evaporated. There was thus obtained ethyl N-tert-butoxycarbonylpiperidine-4-carboxylate (48 g); NMR Spectrum: (CDCl3) 1.25 (t, 3H), 1.45 (s, 9H), 1.55-1.7 (m, 2H), 1.8-2.0 (d, 2H), 2.35-2.5 (m, 1H), 2.7-2.95 (t, 2H), 3.9-4.1 (br s, 2H), 4.15 (q, 2H). A solution of the material so obtained in THF (180 ml) was cooled at 0 C. and lithium aluminium hydride (1M solution in TBF; 133 ml) was added dropwise. The mixture was stirred at 0 C. for 2 hours. Water (30 ml) and 2N aqueous sodium hydroxide solution (10 ml) were added in turn and the mixture was stirred for 15 minutes. The resultant mixture was filtered through diatomaceous earth and the solids were washed with ethyl acetate. The filtrate was washed in turn with water and with brine, dried over magnesium sulphate and evaporated. There was thus obtained N-tert-butoxycarbonyl-4-hydroxymethylpiperidine (36.3 g); NMR Spectrum: (CDCl3) 1.05-1.2 (m, 2H), 1.35-1.55 (m, 10H), 1.6-1.8 (m, 2H), 2.6-2.8 (t, 2H), 3.4-3.6 (t, 2H), 4.0-4.2 (br s, 2H). 1,4-Diazabicyclo[2.2.2]octane (42.4 g) was added to a solution of N-tert-butoxycarbonyl-4-hydroxymethylpiperidine (52.5 g) in tert-butyl methyl ether (525 ml) and the mixture was stirred at ambient temperature for 15 minutes. The mixture was then cooled in an ice-bath to 5 C. and a solution of 4-toluenesulphonyl chloride (62.8 g) in tert-butyl methyl ether (525 ml) was added dropwise over 2 hours while maintaining the reaction temperature at approximately 0 C. The resultant mixture was allowed to warm to ambient temperature and was stirred for 1 hour. Petroleum ether (b.p. 60-80 C., 1L) was added and the precipitate was removed by filtration. The filtrate was evaporated to give a solid residue which was dissolved in diethyl ether. The organic solution was washed in turn with 0.5N aqueous hydrochloric acid solution, water, a saturated aqueous sodium bicarbonate solution and brine, dried over magnesium sulphate and evaporated. There was thus obtained N-tert-butoxycarbonyl-4-(4-toluenesulphonyloxymethyl)piperidine (76.7 g), NMR Spectrum: (CDCl3) 1.0-1.2 (m, 2H), 1.45 (s, 9H), 1.65 (d, 2H), 1.75-1.9 (m, 2H), 2.45 (s, 3H), 2.55-2.75 (m, 2H), 3.85 (d, 1H), 4.0-4.2 (br s, 2H), 7.35 (d, 2H), 7.8 (d, 2H). A portion (40 g) of the material so obtained was added to a suspension of <strong>[617-05-0]ethyl 4-hydroxy-3-methoxybenzoate</strong> (19.6 g) and potassium carbonate (28 g) in DMF (200 ml) and the resultant mixture was stirred and heated to 95 C. for 2.5 hours. The mixture was cooled to ambient temperature and partitioned between water and a mixture of ethyl acetate and diethyl ether. The organic layer was washed in turn with water and brine, dried over magnesium sulphate and evaporated. The resulting oil was crystallised from petroleum ether (b.p. 60-80 C.) and the suspension was stored overnight at 5 C. The resultant solid was collected by filtration, washed with petroleum ether and dried under vacuum. There was thus obtained ethyl 4-(N-tert-butoxycarbonylpiperidin-4-ylmethoxy)-3-methoxybenzoate (35 g), m.p. 81-83 C.; NMR Spectrum: (CDCl3) 1.2-1.35 (m, 2H), 1.4 (t, 3H), 1.48 (s, 9H), 1.8-1.9 (d, 2H), 2.0-2.15 (m, 2H), 2.75 (t, 2H), 3.9 (d, 2H), 3.95 (s, 3H), 4.05-4.25 (br s, 2H), 4.35 (q, 2H), 6.85 (d, 1H), 7.55 (s, 1H), 7.65 (d, 1H). The material so obtained was dissolved in formic acid (35 ml), formaldehyde (12M, 37% in water, 35. ml) was added and the mixture was stirred and heated to 95 C. for 3 hours. The resultant mixture was evaporated. The residue was dissolved in methylene chloride and hydrogen chloride (3M solution in diethyl ether; 40 ml) was added. The mixture was diluted with diethyl ether and the mixture was triturated until a solid was formed. The solid was collected, washed with diethyl ether and dried under vacuum overnight at 50 C. There was thus obtained ethyl 3-methoxy4(N-methylpiperidin-4-ylmethoxy)benzoate (30.6 g), NMR Spectrum: (DMSOd6) 1.29 (t, 3H), 1.5-1.7 (m, 2H), 1.95 (d, 2H), 2.0-2.15 (br s, 1H), 2.72 (s, 3H), 2.9-3.1 (m, 2H), 3.35-3.5 (br s, 2H), 3.85 (s, 3H), 3.9-4.05 (br s, 2H), 4.3 (q, 2H), 7.1 (d, 1H), 7.48 (s, 1H), 7.6 (d, 1H). The material so obtained was dissolved in methylene chloride (75 ml) and the solution was cooled in an ice-bath to 0-5 C. Trifluoroacetic acid (37.5 ml) was added followed by the dropwise addition over 15 minutes... | |
With potassium carbonate; In DMF (N,N-dimethyl-formamide); at 95℃; for 2.5h; | A portion (40 g) of the material so obtained was added to a suspension of <strong>[617-05-0]ethyl 4-hydroxy-3-methoxybenzoate</strong> (19.6 g) and potassium carbonate (28 g) in DMF (200 ml) and the resultant mixture was stirred and heated to 95 C. for 2.5 hours. The mixture was cooled to ambient temperature and partitioned between water and a mixture of ethyl acetate and diethyl ether. The organic layer was washed in turn with water and brine, dried over magnesium sulphate and evaporated. The resulting oil was crystallised from petroleum ether (b.p. 60-80 C.) and the suspension was stored overnight at 5 C. The resultant solid was collected by filtration, washed with petroleum ether and dried under vacuum. There was thus obtained ethyl 4(N-tert-butoxycarbonylpiperidin-4-ylmethoxy)-3-methoxybenzoate (35 g), m.p. 81-83 C.; NMR Spectrum: (CDCl3) 1.2-1.35 (m, 2H), 1.4 (t, 3H), 1.48 (s, 9H), 1.8-1.9 (d, 2H), 2.0-2.15 (m, 2H), 2.75 (t, 2H), 3.9 (d, 2H), 3.95 (s, 3H), 4.05-4.25 (br s, 2H), 4.35 (q, 2H), 6.85 (d, 1H), 7.55 (s, 1H), 7.65 (d, 1H). |
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