Structure of (R)-3-(Boc-amino)pyrrolidine
CAS No.: 122536-77-0
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The BI-3802 was designed by Boehringer Ingelheim and could be obtained free of charge through the Boehringer Ingelheim open innovation portal opnMe.com, associated with its negative control.
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Canale, Vittorio ; Czekajewska, Joanna ; Klesiewicz, Karolina ; Papiez, Monika ; Kuziak, Agata ; Witek, Karolina , et al.
Abstract: The alarming increase in the resistance of bacteria to the currently available antibiotics necessitates the development of new effective antimicrobial agents that are active against bacterial pathogens causing major public health problems. For this purpose, our inhouse libraries were screened against a wide panel of clin. relevant Gram-pos. and Gram-neg. bacteria, based on which compound I was selected for further optimization. Synthetic efforts in a group of arylurea derivatives of aryloxy(1-phenylpropyl) alicyclic diamines, followed with an in vitro evaluation of the activity against multidrug-resistant strains identified compound 44 (1-(3-chlorophenyl)-3-(1-{3-phenyl-3-[3-(trifluoromethyl)phenoxy] propyl}piperidin-4-yl)urea). Compound 44 showed antibacterial activity against Gram-pos. bacteria including fatal drug-resistant strains i.e., Staphylococcus aureus (methicillin-resistant, MRSA; vancomycin-intermediate, VISA) and Enterococcus faecium (vancomycin-resistant, VREfm) at low concentrations (0.78-3.125 μg/mL) comparable to last resort antibiotics (i.e., vancomycin and linezolid). It is also potent against biofilm-forming S. aureus and Staphylococcus epidermidis (including linezolid-resistant, LRSE) strains, but with no activity against Gram-neg. bacteria (Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa). Compound 44 showed strong bactericidal properties against susceptible and drug-resistant Gram-pos. bacteria. Depolarization of the bacterial cytoplasmic membrane induced by compound 44 suggests a dissipation of the bacterial membrane potential as its mechanism of antibacterial action. The high antimicrobial activity of compound 44, along with its selectivity over mammalian cells (lung MCR-5 and skin BJ fibroblast cell lines) and no hemolytic properties toward horse erythrocytes, proposes arylurea derivatives of aryloxy(1-phenylpropyl) alicyclic diamines for development of novel antibacterial agents.
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Keywords: Arylurea derivatives ; Antibacterial properties ; Anti-MRSA activity ; Anti-VRE activity ; Anti-LRSE activity ; Depolarization of bacterial cell membrane
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Purchased from AmBeed: 122536-76-9 ; 936-59-4 ; 135632-53-0 ; 404-71-7 ; 73874-95-0 ; 372-20-3 ; 98-17-9 ; 402-45-9 ; 57260-71-6 ; 122536-77-0 ; 444-30-4 ; 165800-03-3 ; 150-19-6 ; 1195-45-5 ; 2909-38-8 ; 165800-03-3
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| CAS No. : | 122536-77-0 |
| Formula : | C9H18N2O2 |
| M.W : | 186.25 |
| SMILES Code : | O=C(OC(C)(C)C)N[C@H]1CNCC1 |
| MDL No. : | MFCD00143191 |
| GHS Pictogram: |
|
| Signal Word: | Warning |
| Hazard Statements: | H315-H319-H335 |
| Precautionary Statements: | P261-P305+P351+P338 |
| Num. heavy atoms | 13 |
| Num. arom. heavy atoms | 0 |
| Fraction Csp3 | 0.89 |
| Num. rotatable bonds | 4 |
| Num. H-bond acceptors | 3.0 |
| Num. H-bond donors | 2.0 |
| Molar Refractivity | 54.49 |
| TPSA ? Topological Polar Surface Area: Calculated from |
50.36 Ų |
| Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
2.24 |
| Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
0.7 |
| Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
0.49 |
| Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
0.56 |
| Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
0.55 |
| Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
0.91 |
| Log S (ESOL):? ESOL: Topological method implemented from |
-1.17 |
| Solubility | 12.5 mg/ml ; 0.0673 mol/l |
| Class? Solubility class: Log S scale |
Very soluble |
| Log S (Ali)? Ali: Topological method implemented from |
-1.34 |
| Solubility | 8.61 mg/ml ; 0.0462 mol/l |
| Class? Solubility class: Log S scale |
Very soluble |
| Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-1.76 |
| Solubility | 3.21 mg/ml ; 0.0173 mol/l |
| Class? Solubility class: Log S scale |
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 |
Yes |
| 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) |
No |
| CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
No |
| CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
No |
| 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 |
-6.94 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 |
1.0 |
| 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 |
0.0 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) |
2.64 |
* 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 |
|---|---|---|
| With sodium tris(acetoxy)borohydride; In 1,2-dichloro-ethane; at 20℃; for 4.0h; | To a mixture of tert-butyl (R)-pyrrolidin-3-ylcarbamate (50 mg, 0.27 mmol) in 1,2- dichloroethane (1.5 mL) was added benzaldehyde (0.055 mL, 0.54 mmol) followed by NaBH(OAc)3 (171 mg, 0.81 mmol). The mixture was stirred at room temperature for 4 h and then water was added. The mixture was extracted with ethyl acetate, washed with brine, dried over MgSO4, and concentrated in vacuo. To a mixture of crude compound in dichloromethane (3 mL) was added trifluoroacetic acid (0.5 mL). The mixture was allowed to stir overnight and extracted with UCT SPE CUBCX cartridge. The extract was concentrated in vacuo and the crude product was used for the next step without further purification |
[ 34584-69-5 ]
[ 122536-77-0 ]
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 84% | With potassium carbonate; In N,N-dimethyl-formamide; at 110℃; for 7h;Inert atmosphere; | General procedure: Solid K2CO3 (2 equiv) was added to a solution of <strong>[34584-69-5]3,6-dichloro-4,5-dimethylpyridazine</strong> (1 equiv) and amine (1 equiv) in DMF(20 mL), and the resulting solution was stirred at 110 °C for 7 h.The reaction mixture was concentrated under reduced pressure and dissolved in EtOAc, washed with water, dried over magnesium sulfate, filtered, and concentrated in vacuo. The residue was purifiedby silica gel column chromatography (ethyl acetate: hexane= 4:1) to yield pure product. 5.1.1.1. tert-butyl (R)-(1-(6-chloro-4,5-dimethylpyridazin-3-yl)pyrrolidin-3-yl)carbamate (8a). Yellow solid (84percent); 1H NMR (400 MHz,CDCl3) d 4.89 (s, 1H), 4.29 (s, 1H), 3.80?3.61 (m, 2H), 3.57?3.36(m, 2H), 2.30 (s, 3H), 2.24 (s, 3H), 1.96?1.84 (m, 1H), 1.69 (s, 1H),1.43 (s, 9H); MS (ESI+): [M+H]+: 327.2 |
[ 129112-65-8 ]
[ 122536-77-0 ]
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 99% | With N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; for 2.0h; | To a mixture of <strong>[129112-65-8]2,4-dichloro-7-nitroquinazoline</strong> (3.0 g, 12.3 mmol) and (R)-tert-butyl pyrrolidin-3- ylcarbamate (2.3 g, 12.3 mmol) in DCM (50 mL) was added DIEA (4.76 g, 36.9 mmol) at rt and stirred for 2 hrs. The mixture was washed with water (100 mL) and concentrated. The residue was purified by silica gel chromatography (PE:EA = 1.5: 1) to afford (R)-tert-butyl (l-(2-chloro-7- nitroquinazolin-4-yl)pyrrolidin-3-yl)carbamate (4.8 g, 99%) as a yellow solid. [M+H] Calc’d for C17H20CIN5O4, 394.1; Found, 394.1 |

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