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CAS No. : | 110764-79-9 | MDL No. : | |
Formula : | - | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | UVUOJOLPNDCIHL-XKZJCBTISA-N |
M.W : | - | Pubchem ID : | 10897989 |
Synonyms : |
DMT-2'O-Methyl-rU Phosphoramidite
|
Num. heavy atoms : | 54 |
Num. arom. heavy atoms : | 24 |
Fraction Csp3 : | 0.42 |
Num. rotatable bonds : | 18 |
Num. H-bond acceptors : | 11.0 |
Num. H-bond donors : | 1.0 |
Molar Refractivity : | 204.95 |
TPSA : | 160.09 Ų |
GI absorption : | Low |
BBB permeant : | No |
P-gp substrate : | Yes |
CYP1A2 inhibitor : | No |
CYP2C19 inhibitor : | Yes |
CYP2C9 inhibitor : | No |
CYP2D6 inhibitor : | No |
CYP3A4 inhibitor : | Yes |
Log Kp (skin permeation) : | -7.5 cm/s |
Log Po/w (iLOGP) : | 5.02 |
Log Po/w (XLOGP3) : | 4.84 |
Log Po/w (WLOGP) : | 5.7 |
Log Po/w (MLOGP) : | 1.28 |
Log Po/w (SILICOS-IT) : | 5.63 |
Consensus Log Po/w : | 4.5 |
Lipinski : | 2.0 |
Ghose : | None |
Veber : | 2.0 |
Egan : | 1.0 |
Muegge : | 4.0 |
Bioavailability Score : | 0.17 |
Log S (ESOL) : | -6.75 |
Solubility : | 0.000136 mg/ml ; 0.000000179 mol/l |
Class : | Poorly soluble |
Log S (Ali) : | -7.94 |
Solubility : | 0.00000883 mg/ml ; 0.0000000116 mol/l |
Class : | Poorly soluble |
Log S (SILICOS-IT) : | -9.63 |
Solubility : | 0.000000179 mg/ml ; 0.0000000002 mol/l |
Class : | Poorly soluble |
PAINS : | 0.0 alert |
Brenk : | 1.0 alert |
Leadlikeness : | 3.0 |
Synthetic accessibility : | 7.08 |
Signal Word: | Class: | ||
Precautionary Statements: | UN#: | ||
Hazard Statements: | Packing Group: |
* 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 |
---|---|---|
Stage #1: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; DMTrT-CPG Stage #2: With bis-(trimethylsilyl)acetamide; 1,8-diazabicyclo[5.4.0]undec-7-ene In pyridine Further stages.; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; DMTrU-CPG Stage #2: With bis-(trimethylsilyl)acetamide; 1,8-diazabicyclo[5.4.0]undec-7-ene In pyridine Further stages.; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
93 % Chromat. | Multistep reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | Stage #1: With N-ethyl-N,N-diisopropylamine In dichloromethane; toluene for 0.0833333h; Stage #2: With dmap In dichloromethane; toluene for 0.133333h; | 4 General procedure: i) An activated resin obtained in Example 8 (AM-PS-Het5, 250 mg) was loaded into an HPLC column of stainless steel (75 mm x 4.6 mm). The resulting column packed with the activated resin was flushed with toluene at a flow rate of 1.00 mL/min for 15 minutes. The column was weighed (mToiuene + resin + column = 43.118 g), flushed with dichloromethane (DCM) with a flow rate of (0151) 1.00 mL/min for 15 minutes, and then weighted again (rriDCM + res n + column = 43.588 g). The void volume, Vvoid, of the system was determined to establish a connection between flow rate and estimated residence time of the liquid passing through the column. The void volume of the column was calculated using the formula: (0152) Am solvent switch 43.5588 g - 43.118 g (0153) ^void = 1.00 raL (0154) 1 3 0 867 wherein, Arrisoivent switch is the difference in mass and Apsoivent the difference in density when switching solvents, ii) a loaded resin was prepared by loading the activated resin 4 times with PCI (0.10 M) and L/,/V-diisopropylethylamine (DIPEA, 0.10 M) in DCM (2 mL) with flow rate of 1.00 mL/min for 5 minutes including DCM wash, iii) the substrate alcohol (0.10 M, 0.114 mmol) and DMAP (0.15 M, 0.171 mmol) or another base, such as PPY or 9AJ, were dissolved in DCM (1 mL) and eluted through the loaded resin with a flow rate of between 0.125 mL/min and 1.00 mL/min (residence time between 8 minutes and 1 minute), iV) fractions comprising the synthesized phosphoramidites were collected for 2.5 times the residence time. |
100% | Stage #1: With N-ethyl-N,N-diisopropylamine In dichloromethane; toluene for 0.0833333h; Stage #2: With dmap In dichloromethane; toluene for 0.133333h; | 4 General procedure: i) An activated resin obtained in Example 8 (AM-PS-Het5, 250 mg) was loaded into an HPLC column of stainless steel (75 mm x 4.6 mm). The resulting column packed with the activated resin was flushed with toluene at a flow rate of 1.00 mL/min for 15 minutes. The column was weighed (mToiuene + resin + column = 43.118 g), flushed with dichloromethane (DCM) with a flow rate of (0151) 1.00 mL/min for 15 minutes, and then weighted again (rriDCM + res n + column = 43.588 g). The void volume, Vvoid, of the system was determined to establish a connection between flow rate and estimated residence time of the liquid passing through the column. The void volume of the column was calculated using the formula: (0152) Am solvent switch 43.5588 g - 43.118 g (0153) ^void = 1.00 raL (0154) 1 3 0 867 wherein, Arrisoivent switch is the difference in mass and Apsoivent the difference in density when switching solvents, ii) a loaded resin was prepared by loading the activated resin 4 times with PCI (0.10 M) and L/,/V-diisopropylethylamine (DIPEA, 0.10 M) in DCM (2 mL) with flow rate of 1.00 mL/min for 5 minutes including DCM wash, iii) the substrate alcohol (0.10 M, 0.114 mmol) and DMAP (0.15 M, 0.171 mmol) or another base, such as PPY or 9AJ, were dissolved in DCM (1 mL) and eluted through the loaded resin with a flow rate of between 0.125 mL/min and 1.00 mL/min (residence time between 8 minutes and 1 minute), iV) fractions comprising the synthesized phosphoramidites were collected for 2.5 times the residence time. |
60% | 58 5'-O-(4,4'-dimethoxytriphenylmethyl)-2'-O-methyluridine-3'-O-(β-cyanoethyl N,N-diisopropylphosphoramidite) Example 58 5'-O-(4,4'-dimethoxytriphenylmethyl)-2'-O-methyluridine-3'-O-(β-cyanoethyl N,N-diisopropylphosphoramidite) The product was prepared as per Example 54 from the intermediate 5'-O-(4,4'-dimethoxytriphenylmethyl)-2'-O-methyl-uridine. Ethyl acetate-hexanes-triethylamine (59:40:1) was used as the chromatography eluent to give the product as a solid foam in 60% yield. TLC homogenous diastereomers, Rf 0.58; 0.44 [ethyl acetate-hexanes-triethylamine 59:40:1)]. 31 P-NMR (CDCl3, H3 PO4 std.) d 148.11; 148.61 (diastereomers). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With ammonia In water at 55℃; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-dimethoxytrityl-2'-[(dodecanoyl)amino]-2'-deoxyuridine-3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite); 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) Automated synthesizer; solid phase reaction; Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With ammonia In water at 55℃; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-dimethoxytrityl-2'-[(dodecanoyl)amino]-2'-deoxyuridine-3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite); 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) Automated synthesizer; solid phase reaction; Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With ammonia In water at 55℃; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-dimethoxytrityl-2'-[(dodecanoyl)amino]-2'-deoxyuridine-3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite); 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) Automated synthesizer; solid phase reaction; Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With ammonia In water at 55℃; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-dimethoxytrityl-2'-[(dodecanoyl)amino]-2'-deoxyuridine-3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite); 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) solid phase reaction; Automated synthesizer; Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With ammonia In water at 55℃; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) Automated synthesizer; solid phase reaction; Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
64% | Stage #1: C10H13N2O5Pol; 5'-O-dimethoxytritil-2'-O-methylguanosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) With benzimidazolium trifluoromethanesulfonate In acetonitrile at 20℃; for 0.166667h; Automated synthesizer; solid phase reaction; Stage #2: With 1-methyl-pyrrolidin-2-one; 1-hydroxy-6-nitro-1,2,3-benzotriazole In acetonitrile at 20℃; for 0.0333333h; Automated synthesizer; solid phase reaction; Stage #3: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine; 5'-O-dimethoxytritil-2'-O-methylcytidine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite); 5'-O-dimethoxytritil-2'-O-methyladenosine-3'-O-(2-cianoethyl-N,N-diisopropylphosphoramidite) Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: C24H30N8O11PPol; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With benzimidazolium trifluoromethanesulfonate In acetonitrile at 20℃; for 0.166667h; solid phase reaction; Stage #2: With 1-methyl-pyrrolidin-2-one; 1-hydroxy-6-nitro-1,2,3-benzotriazole In acetonitrile at 20℃; for 0.0333333h; solid phase reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: C23H30N6O12PPol; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With benzimidazolium trifluoromethanesulfonate In acetonitrile at 20℃; for 0.166667h; solid phase reaction; Stage #2: With 1-methyl-pyrrolidin-2-one; 1-hydroxy-6-nitro-1,2,3-benzotriazole In acetonitrile at 20℃; for 0.0333333h; solid phase reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: C16H18N3O8Pol; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With benzyl tetrazol-5-yl sulphide In acetonitrile at 20℃; for 0.5h; solid phase reaction; Stage #2: With pyridine; water; iodine In tetrahydrofuran solid phase reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: C44H50N3O8PolSi With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With iodine Automated synthesizer; solid phase reaction; Stage #3: C50H67N8O7P; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: C44H50N3O8PolSi With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With iodine Automated synthesizer; solid phase reaction; Stage #3: C49H67N6O8P; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
27% | Stage #1: C44H50N3O8PolSi With 1H-tetrazole Automated synthesizer; solid phase reaction; Stage #2: With iodine Automated synthesizer; solid phase reaction; Stage #3: C58H87N6O9PSi; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine Further stages; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With benzyl tetrazol-5-yl sulphide In acetonitrile for 0.166667h; Automated synthesizer; solid phase reaction; Stage #2: With water; iodine In pyridine Automated synthesizer; solid phase reaction; Stage #3: With ammonium hydroxide In water Automated synthesizer; solid phase reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Multi-step reaction with 2 steps 1.1: 1H-tetrazole / acetonitrile / 2 h / 20 °C 1.2: 1 h 2.1: ammonia / methanol / 1 h / 20 °C |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Multi-step reaction with 3 steps 1.1: 1H-tetrazole / acetonitrile / 2 h / 20 °C 1.2: 1 h 2.1: ammonia / methanol / 1 h / 20 °C 3.1: hydrogenchloride; water / 6 h / 20 °C 3.2: Dowex 50Wx8 (Na+) resin |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
70% | Stage #1: 3'-O-(tert-butyldiphenylsilyl)-2'-O-methyl-5'-C-(2-tosyloxyethyl)uridine; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With 1H-tetrazole In acetonitrile at 20℃; for 2h; Stage #2: With water; iodine In tetrahydrofuran |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With 5-(ethylthio)-1H-tetrazole In acetonitrile Inert atmosphere; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With 5-(ethylthio)-1H-tetrazole In acetonitrile solid phase reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 5-(prop-2-yn-1-yloxy)-1,2-dithian-4-ol; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With 5-(ethylthio)-1H-tetrazole In acetonitrile at 20℃; for 1h; Stage #2: With tert.-butylhydroperoxide In decane; acetonitrile for 3h; | Compound 2 Compound 25 ‘-O-[bis(4-methoxyphenyl)(phenyl)methyll -3 ‘-O-[(2-cyanoethoxy) [(4S/R,5R/S)-5 -(prop-2-yn-1 -yloxy)- 1 ,2-dithian-4-ylloxyH,hosphoryll-2’-O-methyluridine. A mixture of 5’-O-[bis(4- methoxyphenyl)(phenyl)methyl] -3 ‘-0- [(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2’- 0-methyluridine (2 .74g, 3.60 mmol) and (4S/R, 5R/S)-5 -(prop-2-yn- 1 -yloxy)- 1 ,2-dithian-4-ol (Intermediate 1, 0.685g, 3.60 mmol) was co-evaporated with toluene (3 x 200mL) and dissolved in acetonitrile (2OmL). Solid thioethyl tetrazole (0.47g, 3.60 mmol) was added andthe solution was stirred at ambient temperature for lh. A solution of tert-butyl hydroperoxide(800iL, 4.40 mmol, 5.5M in decane) was added and stirring continued for additionla 3 hours.The reaction mixture was poured onto lOOmL of 10% sodium thiosulfate and extracted withdichloromethane (3 x 1 OOmL). Combined organic extracts were back washed with water (1 x1 OOmL) and brine (1 x 1 OOmL), dried (anhydrous sodium sulfate) and the solvent wasremoved in vacuo to yield the desired product as a mixture of four isomeres. LCMS: for C41H44N3012P52 calculated 865.21, found 888.1 [M + Na]. 31P NMR (600 MHz, CD3CN) ö:-2.47, -2.66, -2.70, -3.06. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Stage #1: 2’-deoxy-2’-fluoro-3’-O-(tert-butyldimethylsilyl)uridine; 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(dipropan-2-ylamino)phosphanyl]-2'-O-methyluridine With 5-(ethylsulfanyl)-2H-tetrazole In dichloromethane for 2.5h; Stage #2: With 2,6-dimethylpyridine In dichloromethane for 4h; | 2.B-1 Synthesis of chirally pure 2’-OMe uridine- 2’F-uridine phosphorothioate dinucleotide (UOMeSUF) phosphoramidite building block (usUf) Compound 10: Compound 8 (11.18 g, 14.7 mmol) and compound 9 (5.55 g, 15.4 mmol, 1.05 eq.) were dried under high vacuum and dissolved in 350 ml dichloromethane (dry). To this solution was added 117 ml ETT (3.83 g, 29.4 mmol, 2 eq.), and the reaction mixture was stirred for 2.5 hours. PADS (6.35 g, 22.05 mmol, 1.5 eq.) and 2.52 ml 2.6-lutidine (2.36 g, 22.05 mmol, 1.5 eq.) were added, and the reaction mixture was stirred for 4 hours. The reaction mixture was diluted with 800 ml dichloromethane and washed with 0 (300 ml) twice. The organic layer was dried over anhydrous NazSCri and concentrated. The diastereomers were separated on CombfFlash column (330 g column, EtOAc: n-hexane (4: 1)) to yield 10a (top spot: 3.37 g, 22%) and 10b (lower spot: 6.3 g, 41%). In EtOAc: n-hexane (4: 1), 10a (Rf = 0.5) and 10b (Rf = 0.23). (0797) 10a MR (400 MHz, acetonitrile-A) d 7.90 (d, J= 8.1 Hz 1H), 7.61 (d , J= 8.1 Hz, 1H), 7.43 - 7.38 (m, 2H), 7.35 - 7.22 (m, 7H), 6.91 - 6.84 (m, 4H), 5.96 (d, J= 3.9 Hz, 1H), 5.85 (dd, J= 19.3, 2.1 Hz, 1H), 5.65 (d, J= 8.0 Hz, 1H), 5.27 - 5.19 (m, 2H), 5.10 (ddd, J= 53.1, 4.8, 2.1 Hz, 1H), 4.53 - 4.40 (m, 2H), 4.34 - 4.22 (m, 2H), 4.18 - 4.10 (m, 3H), 4.06 - 3.98 (m, 1H), 3.78 (s, 6H), 3.58 (dd, J= 11.2, 3.0 Hz, 1H), 3.51 (s, 3H), 3.48 (dd, J= 11.1, 2.9 Hz, 1H), 2.71 (q, J= 6.1 Hz, 2H), 0.91 (s, 9H), 0.14 (d, J= 4.8 Hz, 6H). 13C NMR (126 MHz, CD3OD) 5 166.07, 165.91, 160.01, 152.27, 151.88, 146.40, 143.10, 143.08, 142.11, 137.34, 131.21, 129.29, 128.67, 127.67, 124.20, 118.61, 113.98, 113.85, 103.30, 103.18, 94.14, (0798) 94.09, 92.62, 92.58, 91.62, 91.59, 91.34, 91.31, 87.83, 87.79, 87.70, 85.34, 85.30, 82.97, 82.87, 82.79, 77.47, 77.43, 77.39, 70.90, 70.77, 67.47, 67.42, 64.57, 64.53, 61.95, 59.28, (0799) 59.26. 55.71. 55.67. 26.16, 19.99, 19.92, 18.92, -4.61, -4.79. 31P NMR (162 MHz, CD3CN) d 67.12. 19F NMR (376 MHz, CD3OD) d -209.65, -209.70, -209.75, -209.80, -209.84, -209.89, -210.14, -210.18, -210.23, -210.28, -210.32, -210.37. Molecular weight for (0800) C49H59FN5Oi4PSSi (M+Na): calculated 1074.3168, found 1074.3146. (0801) 10b NMR (400 MHz, acetonitrile^) d 7.93 (d, J= 8.1 Hz, 1H), 7.49 (d, J= 8.1 Hz, 1H), 7.41 (d, J= 7.4 Hz, 2H), 7.32 - 7.22 (m, 7H), 6.87 (dd, J= 9.0, 2.4 Hz, 4H), 5.94 (d, J= 3.7 Hz, 1H), 5.73 (dd, J = 20.3, 1.4 Hz, 1H), 5.61 (d, J= 8 1 Hz, 1H), 5.30 - 5.17 (m, 2H), 5.16 - 4.98 (m, 1H), 4.52 - 4.40 (m, 1H), 4.35 - 4.23 (m, 3H), 4.19 - 4.08 (m, 4H), 4.01 - 3.94 (m, 1H), 3.77 (s, 6H), 3.54 (s, 4H), 2.88 (t, J= 5.8 Hz, 2H), 0.91 (s, 9H), 0.13 (d, j= 3.6 Hz, 6H). 13C NMR (126 MHz, CD3OD) d 165.98, 165.87, 160.41, 160.37, 151.95, 151.71, 145.68, 143.24, 141.78, 136.26, 131.67, 131.60, 131.23, 129.57, 129.31, 129.01, 128.67, 128.25, 118.62, 114.30, 114.29, 113.99, 103.10, 102.90, 94.22, 92.72, 92.28, 91.99, 88.61, 88.59, (0802) 83.16, 83.14, 82.78, 82.72, 82.36, 82.29, 75.76, 75.73, 70.56, 70.43, 67.12, 67.08, 64.68, 64.64, 62.40, 59.21, 55.77, 26.19, 20.85, 20.02, 19.96, 18.92, -4.57, -4.76. 31P NMR (202 MHz, CD3CN) d 67.90. 19F NMR (376 MHz, CD3OD) d -208.37, -208.43, -208.48, -208.52, - 208.57, -208.62, -208.77, -208.82, -208.87, -208.91, -208.96, -209.01. Molecular weight for C49H59FN5Oi4PSSi (M+Na): calculated 1074.3168, found 1074.3157. |
Yield | Reaction Conditions | Operation in experiment |
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Compound 3: Compound 1 (11.18 g, 14.7 mmol) and compound 2 (5.73 g, 15.4 mmol, 1.05 eq.) were dried under high vacuum and dissolved in 150 ml dichloromethane (dry). To this solution 117 ml ETT (3.83 g, 29.4 mmol, 2 eq.) was added and the reaction mixture was stirred for 2.5 hours. PADS (6.35 g, 22.05 mmol, 1.5 eq.) and 2.52 ml 2.6-lutidine (2.36 g, 22.05 mmol, 1.5 eq.) were added, and the reaction mixture was stirred for 4 hours. The reaction mixture was diluted with 800 ml dichloromethane and washed with ThO (300 ml) twice. The organic layer was dried over anhydrous Na2S04 and concentrated. The diastereomers were separated on CombiFlash (330g column, EtOAc: n-hexane (4: 1), 3a Rf (top spot) = 0.45, 3b Rf (lower spot) = 0.24) to yield 3a (9.12 g, 56%) and 3b (6.7 g, 43%). (0759) 3a ^ NMR (500 MHz, acetonitrile-i) d 9.17 (s, 2H), 7.65 (d, J= 8.2 Hz, 1H), 7.59 (d, J = 8.2 Hz, 1H), 7.46 (d, j= 7.4 Hz, 2H), 7.40 - 7.27 (m, 8H), 6.92 (d, j= 8.8 Hz, 4H), 5.94 (d, J = 4.8 Hz, 1H), 5.85 (d, J= 3.4 Hz, 1H), 5.66 (d, .7= 8.1 Hz, 1H), 5.35 (d, J= 8.1 Hz, 1H), (0760) 5.25 - 5.16 (m, 1H), 4.51 - 4.40 (m, 1H), 4.36 - 4.10 (m, 7H), 3.80 (s, 6H), 3.48 (s, 3H), 3.46 (s, 3H), 3.45 - 3.43 (m, 2H), 2.75 - 2.70 (m, 2H), 0.93 (s, 9H), 0.14 (s, 6H). 13C NMR (126 MHz, CD3CN) 5 163.95, 163.75, 159.91, 151.37, 151.34, 145.52, 141.03, 140.88, 136.38, 136.24, 131.22, 131.21, 130.46, 129.46, 129.18, 129.07, 128.18, 121.08, 114.29, 114.28, 103.23, 102.99, 89.11, 88.03, 87.83, 83.63, 82.95, 82.87, 82.71, 82.65, 82.31, 82.28, 76.06, 76.03, 70.88, 68.10, 68.05, 64.32, 64.29, 62.99, 59.23, 58.87, 56.04, 26.15, 20.16, 20.09, 18.75, 15.39, -4.36, -4.62. 31P NMR (162 MHz, CD3CN) d 68.77. Molecular weight for CsoHeiNsOisPSSi (M+Na): calculated 1086.3368, found 1086.3392. (0761) 3b NMR (500 MHz, acetonitrile-u) d 9.09 (s, 2H), 7.67 (d, J= 8.2 Hz, 1H), 7.49 (dd, J = 21.3, 7.8 Hz, 3H), 7.34 (d, J= 8.9 Hz, 8H), 7.06 (d, J= 7.7 Hz, 1H), 6.91 (d, J= 8.9 Hz, 4H), 5.93 (d, J= 4.7 Hz, 1H), 5.81 (d, = 3.2 Hz, 1H), 5.64 (d, .7= 8.1 Hz, 1H), 5.33 (d, .7= 8.1 Hz, 1H), 5.26 - 5.17 (m, 1H), 4.33 - 4.20 (m, 6H), 4.13 - 4.09 (m, 1H), 4.07 - 4.03 (m, 1H), 3.80 (s, 6H), 3.52 (s, 3H), 3.45 (s, 3H), 3.43 (d, J= 3.0 Hz, 2H), 2.84 (t, J= 5.8 Hz, 2H), 0 92 (s, 9H), 0.12 (s, 6H). 13C NMR (126 MHz, CD3CN) d 163.89, 163.73, 159.90, 159.89, 151.37, 151.28, 145.59, 141.00, 140.92, 138.31, 136.33, 136.20, 131.25, 131.23, 129.15, 129.05, 128.14, 121.34, 114.26, 114.26, 103.17, 102.98, 89.20, 88.01, 87.95, 83.59, 82.78, 82.71, 82.67, 82.62, 82.43, 82.40, 75.97, 75.93, 70.66, 67.77, 67.72, 64.57, 64.54, 62.87, 59.28, 58.83, 56.02, 26.16, 20.22, 20.15, 18.74, 15.39, -4.34, -4.61. 31P NMR (162 MHz, CD3CN) d 69.27 Molecular weight for CsnHiaN OisPSSi (M+Na): calculated 1086.3368, found 1086.3392. |
Yield | Reaction Conditions | Operation in experiment |
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89% | As illustrated herein, phosphoramidate internucleotidic linkages can be readily prepared from phosphite internucleotidic linkages, including stereopure phosphite internucleotidic linkages, in accordance with the present disclosure. To a stirred solution of amidite (474 mg, 0.624 mmol, 1.5 equiv., pre-dried by co evaporation with dry acetonitrile and under vacuum for a minimum of 12 h) and TBS protected alcohol (150 mg, 0.41 mmol, pre-dried by co-evaporation with dry acetonitrile and under vacuum for a minimum of 12 h) in dry acetonitrile (5.2 ml) was added 5-(et hylthio)-///-tctrazolc (ETT, 2.08 ml, 0.6M, 3 equiv.) under argon atmosphere at room temperature. The reaction mixture was stirred for 5 mins then monitored by LCMS and then a solution of 2-azido-l,3- dimethylimidazolinium hexafluorophosphate (356 mg, 1.24 mmol, 3 equiv.) in acetonitrile (1 ml) was added. Once the reaction was completed (after ~ 5 mins, monitored by LCMS) then triethylamine (0.17 ml, 1.24 mmol, 3 equiv) was added and the reaction was monitored by LCMS. The reaction mixture was concentrated under reduced pressure and then redissolved in dichloromethane (50 ml), washed with water (25 ml), saturated aq. sodium bicarbonate (25 ml), and brine (25 ml), and dried with magnesium sulfate. The solvent was removed under reduced pressure. The crude product was purified by silica gel column (80 g) using DCM (5% triethyl amine) and MeOH as eluent. Product-containing fractions were collected and the solvent was evaporated. The resulted product may contain TEA.HC1 salt. To remove the salt, the product was re-dissolved in DCM (50 ml) and washed with saturated aq. sodium bicarbonate (20 ml) and brine (20 ml) then dried with magnesium sulfate and the the solvent was evaporated. A pale yellow solid was obtained. Yield: 440 mg (89%). 31P NMR (162 MHz, CDCl3) d -1.34, -1.98. MS calculated for C5iH65PN70i4PSi [M]+ 1078.17, Observed: 1078.57 [M + H]+. |
Yield | Reaction Conditions | Operation in experiment |
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With 1H-tetrazole In acetonitrile at 20℃; for 3h; Inert atmosphere; | 7 [Example 7] Synthesis of compound 3g Add 5'-O-(4,4'-dimethoxytrityl)-2'-O-methyluridine-3'-O-(2-cyanoethyl-N,N-di Isopropyl) phosphoramidite (compound 1c, 287mg, 0.370mmol) was added to 20mL of 1H-tetrazole (52mg, 0.743mmol) in anhydrous acetonitrile, under the protection of argon, 2,3-hexadecanol was added -1-glyceryl ether (200mg, 0.370mmol), stirred at room temperature for 3h, then added diphenylacetyl disulfide (224mg, 0.817mmol), stirred at room temperature for 6h. After that, the solvent was removed by rotary evaporation, and the residue was redissolved in methylamine/ethanol (33%, 20 mL), and stirred at room temperature for 4 h. Then, the solvent was removed by rotary evaporation, and the residue was redissolved in TFA/DCM (v:v, 10%, 20 mL), and stirred at 0°C for 30 min. The product was purified by column chromatography with dichloromethane/methanol (v:v, 20:1) as the elution solvent. A white solid (compound 3g, 195mg, 0.222mmol) was obtained with a yield of 60% |