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Structure of 534-03-2
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Solubilizer Tag Effect on PD-L1/Inhibitor Binding Properties for m-Terphenyl Derivatives
Surmiak, Ewa ; Zaber, Julia ; Plewka, Jacek ; Wojtanowicz, Grzegorz ; Kocik-Krol, Justyna ; Kruc, Oskar , et al.
Abstract: Although heavily studied, the subject of anti-PD-L1 small-mol. inhibitors is still elusive. Here, we present a systematic overview of the principles behind the successful anti-PD-L1 small mol. inhibitor design on the example of the m-terphenyl scaffold with a particular focus on the neglected influence of the solubilizer tag on the overall affinity toward PD-L1. The inhibitor developed according to the proposed guidelines was characterized through its potency in blocking the PD-1/PD-L1 complex formation in HTRF and cell-based assays. The affinity is also explained based on the crystal structure of the inhibitor itself, its costructure with PD-L1 as well as mol. modeling study. Our results structuralize the knowledge related to the strong pharmacophore feature of the m-terphenyl scaffold preferential geometry and the more complex role of the solubilizer tag in PD-L1 homodimer stabilization.
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Keywords: PD-L1 ; Immune checkpoint ; Small-molecule inhibitor ; Cancer ; m-Terphenyl
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CAS No. : | 534-03-2 |
Formula : | C3H9NO2 |
M.W : | 91.11 |
SMILES Code : | OCC(N)CO |
MDL No. : | MFCD00051487 |
InChI Key : | KJJPLEZQSCZCKE-UHFFFAOYSA-N |
Pubchem ID : | 68294 |
GHS Pictogram: |
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Signal Word: | Danger |
Hazard Statements: | H314 |
Precautionary Statements: | P501-P260-P264-P280-P303+P361+P353-P301+P330+P331-P363-P304+P340+P310-P305+P351+P338+P310-P405 |
Class: | 8 |
UN#: | 3259 |
Packing Group: | Ⅲ |
Num. heavy atoms | 6 |
Num. arom. heavy atoms | 0 |
Fraction Csp3 | 1.0 |
Num. rotatable bonds | 2 |
Num. H-bond acceptors | 3.0 |
Num. H-bond donors | 3.0 |
Molar Refractivity | 21.57 |
TPSA ? Topological Polar Surface Area: Calculated from |
66.48 ?2 |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
0.73 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
-2.02 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
-1.7 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
-1.51 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
-1.2 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
-1.14 |
Log S (ESOL):? ESOL: Topological method implemented from |
1.0 |
Solubility | 911.0 mg/ml ; 9.99 mol/l |
Class? Solubility class: Log S scale |
Highly soluble |
Log S (Ali)? Ali: Topological method implemented from |
1.15 |
Solubility | 1280.0 mg/ml ; 14.1 mol/l |
Class? Solubility class: Log S scale |
Highly soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
0.87 |
Solubility | 669.0 mg/ml ; 7.35 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 |
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) |
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 |
-8.29 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 |
3.0 |
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) |
1.0 |
* 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 |
---|---|---|
100% | In ethanol; at 20℃; for 16h; | To a solution of 2-anunopropane-1 ,3-diol (1 0. 0 g, 0.1 mol) in EtOH ( 100 mL) wasadded di-tert-butyl dicarbonate (24.0 g, 0.1 mol). The reaction was stirred at room temperaturefor 16 hrs. The reaction solution was concentrated in vacuo to dryness to give tert-butyl (1,3-dihydroxypropan-2-yl)carbamate (21.0 g, yield: 1 00'%) as a white solid. |
97% | In dichloromethane; at 22 - 25℃; for 4h; | Serinol (2.00 g, 21.96 mmol) and (Boc)20 (4.80 g, 21.96 mmol) was dissolved in 20 mL of dichloromethane. The reaction mixture was stirred for 4 h at 22 to 25 C. The above mixture was washed with water (25 mL x 2), dried over anhydrous sodium sulfate and concentrated under vacuum toyield tert-butyl (1 ,3-dihydroxypropan-2-yl)carbamate (4.1 g, 97% yield). |
95% | With hydrogenchloride; In 1,4-dioxane; water; at 20℃;Cooling with ice; | Serinol (10.1 mmol) (manufactured by Aldrich Chem. Co.) was dissolved in water-dioxane (1:1, 20 ml), andthen a dioxane solution (15 ml) of Boc2O (10.8 mmol) was added thereto under ice-cooling, followed by stirring overnightwhile returning to room temperature. The solvent was evaporated under reduced pressure. The residue was washedwith hexane and then dried under reduced pressure to give the titled compound (1847 mg, yield 95%).The structurewas identified by 1H-NMR.1H-NMR (500 MHz, CD3OD) delta (ppm) = 1.44 (9H, s, Boc), 3.57-3.58 (5H, m, Serinol) |
95% | With trimethylamine; In dichloromethane; for 4h; | Serinoi (2,00 g, 22,0 mmol) was dissolved in dichioromethane (40 mL) and trimethylamitie (10 mL). Di-tert-butyl dicarbonate (5.76 g, 26.4 mmol, 1.2 eq) was then added, and the reaction stirred for 4 hours. The mixture was evaporated and the residue portioned between ethyl acetate and water. The organic fraction was washed with water ( lx), 1M HC1 (2x), saturated sodium bicarbonate (lx), and brine (lx) before drying over sodium sulfate and evaporation to give compound 23 (3.99 g, 20.9 mmol) in 95% yield, which was used without purification in further steps. |
91% | In ethanol; at 20℃; for 6h; | 2-amino-1,3-propanediol (5 g) was dissolved in 150 mL of absolute ethanol, A solution of 100 mL of Boc anhydride (12 g) in absolute ethanol was added, Room temperature reaction 6h, Remove the solvent, Recrystallization from n-heptane gave a white solid 3 (9.6 g, 91%). |
72% | With N-ethyl-N,N-diisopropylamine; In methanol; for 0.25h;Product distribution / selectivity; | Example 2Lambda/-Boc-Serinol. Lambda/,Lambda/-diisopropylethylamine (DIEA; 10.3 ml_, 59 mmol, 1.1 equiv) was added to serinol (4.88 g, 54 mmol, 1 equiv) in 10 ml_ methanol. A solution of di-f-butyl dicarbonate (12.9 g, 59 mmol, 1.1 equiv.) in 5 mL methanol was then added to the original solution. The reaction was exothermic and evolved gas. The reaction appeared to be complete after 15 min. (as determined by TLC analysis in 9:1 CHCI3:CH3OH with ninhydrin stain). The solvent was then removed at reduced pressure, and the crude material was purified by flash chromatography, using CHCI3:CH3OH (first at a 9:1 ratio and then at a 85:15 ratio), to yield 7.18g (72% yield) of white, flaked crystals. [Rf: 0.35 (5:1 CHCI3:CH3OH); melting point 85-860C; 1H NMR (200 MHz, CDCI3) delta 5.25 (br d, J = 5.6, 1 H, NH), 3.9-3.65 (m, 5H, (-CH2)2CH-), 2.62 (t, J = 5.6, 2H, OH), 1.45 (s, 9H, C(CHa)3)]. EPO <DP n="30"/>Example 3[0107] To prepare the bis-phthalonitrile used in scheme 2, the nitrogen of serinol was Boc-protected, and the serinol was then reacted with 3-nitrophthalonitrile on a multi-gram scale, to give the desired tethered bis-phthalonitrile, in 70% yield |
62% | With potassium carbonate; In tetrahydrofuran; water; at 20℃; | 2-Amino-1,3-propanediol (1.62 g, 17.8 mmol, 1.0 eq) was dissolved in 60 mL of tetrahydrofuran/H2O (1/1). Di-tert-butyl dicarbonate (Boc2O) (5.82 g, 26.7 mmol, 1.5 eq) and K2CO3 (6.15 g, 44.5 mmol,2.5 eq) were added. The reaction was stirred at room temperature overnight. The reaction systemwas allowed to stand for stratification, and the aqueous phase was extracted three times withtetrahydrofuran. The organic phase was combined, dried over anhydrous Na2SO4, evaporatedin vacuo, and puried by column chromatography (silica gel:petroleum ether/ethyl acetate, 1:1) toproduce compound 4 as a white solid in a 62% yield (2.1 g, 11.0 mmol). 1H-NMR (400 MHz, CDCl3) 5.24 (s, 1H), 3.81 (qd, J = 11.1, 4.3 Hz, 4H), 3.69 (s, 1H), 2.50 (dd, J = 22.1, 14.7 Hz, 2H), 1.46 (s, 9H),which agrees with published data [39]. |
49% | With triethylamine; In tetrahydrofuran; at 0 - 20℃; | 2-Amino-1 ,3-propanediol (5.Og, 54.9mmol) was dissolved in dry THF (175ml) and triethylamine (7.7ml) added. The solution was cooled in an ice-bath and di-fe/f- butylcarbonate (11.98g, 54.9mmol) added in portions over 15mins. The solution was allowed to warm to ambient temperature and stirred for 90mins. The solvent was evaporated and water (250ml) added and the product extracted into ethyl acetate (4 x 125ml). The combined organics were washed with brine, dried over magnesium sulphate, filtered and evaporated. The product was isolated by recrystallization from hot ethyl acetate-petrol (1 :3) to give shiny flakes 5.18g (49% yield). The structure was confirmed by 1H NMR (300MHz , CDCI3): 1.44 (s, 9H), 3.08-3.17 (m, 1 H), 3.61 - 3.84 (m, 4H). |
With triethylamine; In dichloromethane; at 20℃;Cooling with ice; | General procedure: Diols or diamine (0.048 mol) and triethylamine (4.81 g, 0.057 mol) were dissolved in anhydrous CH2Cl2 (50 mL). (Boc)2O (12.45 g, 0.057 mol) in anhydrous CH2Cl2 solution was added dropwise to the above stirred solution under the ice bath. The mixture was stirred overnight at room temperature, followed by evaporation of the organic solvents. The residue was purified with silica gel column chromatography (dichloromethane/methyl alcohol = 30: 1). The synthesis of naked two primary amine compound according to the literature [29]. Then, acryloyl chloride (6.95 g, 0.077 mol) in anhydrous dichloromethane (50 mL) was added dropwise to a stirred solution of diol or diamine (0.038 mol) and triethylamine (7.77 g, 0.077 mol) in anhydrous dichloromethane (50 mL) under the ice bath. The mixture was stirred overnight at room temperature and then filtered off generated salt, followed by evaporation of the volatile solvent. The residue was purified with silica gel column chromatography (PE: EA = 3: 1, v/v) to give LC1-LC6. | |
With triethylamine; In dichloromethane; at 0 - 20℃; | General procedure: Diethanolamine 3 (or threoninol 5, 3-amino-1,2-propanediol 6)(0.047 mol) was dissolved in CH2Cl2 and triethylamine (9.60 g,0.095 mol) was slowly added. The solution was cooled to 0 C,and (Boc)2O (12.45 g, 0.057 mol) was added dropwise. Then themixed solution was left for stirring at room temperature overnight.The solvent was removed under reduce pressure to afford crudeproduct, which was further purified by silica gel column chromatography(CH2Cl2/CH3OH = 10/1, v/v) to give compound 3a (or5a, 6a). | |
With triethylamine; In dichloromethane; | Referring to Scheme LLL, the amino group in diol 1-29 is protected with Boc2O to provide compound 1-30 which is mesylated (e.g., with MsC1 and TEA) to afford compound 1-31. Compound 1-31 is subjected to a double nucleophilic substitution with pyrazolone 1-9, providing1-32, which is brominated (e.g., with NBS) to afford compound 1-33. Sequential treatment of 1-33 with n-butyl lithium, zinc chloride, and TCPC provides compound 1-34. Intermediate 61 is obtained when 1-34 is reacted with aqueous ammonia. | |
In methanol; water; at 0 - 25℃; for 4.5h; | Add 6mL of deionized water and 14mL of methanol to the three-necked flask, stir and mix well, then add 0.02mol serinol to the mixed solution, stir and dissolve it completely, cool to 0 C with an ice bath, and then add the three mixed solutions Slowly add 0.022mol of di-tert-butyl dicarbonate. During the dropwise addition, the temperature was maintained at 0 C. After 30 minutes, the ice bath was removed and the reaction was performed at a constant 25 C for 4 hours. After the reaction was completed, extraction was performed three times with dichloromethane. The solvent methanol and water were distilled off under reduced pressure, and vacuum-dried at 45 C. for 24 h to obtain the product tert-butyl 1,3-dihydroxypropane-2-carbamate. | |
With triethylamine; In dichloromethane; for 4h; | Serinol (2.00 g, 22.0 mmol) was dissolved in dichloromethane (40 mL) and trimethyamine ( 10 mL). Di-tert-butyl dicarbonate (5.76 g, 26.4 mmol, 1 .2 eq) was then added, and the reaction stirred for 4 hours. The mixture was evaporated and the residue portioned between ethyl acetate and water. The organic fraction was washed with water ( l x), 1 M HCI (2x), saturated sodium bicarbonate ( l x), and brine ( l x) before drying over sodium sulfate and evaporation to give compound 23 (3.99 g, 20.9 mmol) in 95% yield, which was used without purification in further steps. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
94% | In ISOPROPYLAMIDE; at 8 - 20℃; for 10h; | 680 g of S-(-)-5-((2-acetyloxy)-1-oxopropyl)amino)-2,4,6-triiodo-1,3-benzendicarboxylic acid dichloride (prepared as described in WO 96/37460) are dissolved in 1360 g of dimethylacetamide at room temperature and after cooling at 15C [Solution A ]. 181 g of 2-ammino-1,3-propanediol purified with the method described in the previous Example 1 are dissolved in 1360 g of dimethylacetamide and added to the solution A in one hour at 8-15C whilst stirring. The reaction is completed after ten hours at room temperature. The reaction mixture is concentrated at 100C at 10 mbar until 98% of the solvent is distilled. 1700 g of water are added to the residue and the solution is purified using the method described in WO 97/30735.Yield on dry Iopamidol: 94% Contents of by-products determined with HPLC method (according to the method described in USP XXIII-NF, 1996, Vsuppl.) = 0.11% The by-product N-[2-hydroxy-1-(hydroxymethyl)ethyl]-- N'-(2,3-dihydroxypropyl)-5-(2-hydroxy-1-oxopropyl)-2,4,6-triiodo-1,3-benzenedicarboxamide, coming from isoserinol, is under the detection limit. No presence of other by-products derived from 3-amino-1,2-propanediol are detected (see as ref. Pharmeuropa, 6, 343-345, 19949. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
49% | With triethylamine; In tetrahydrofuran; at 0 - 20℃; for 1.75h; | Preparation J(2-Hydroxy-1-hvdroxymethyl-ethyl)-carbamic acid tert-butyl esterO H ^OH <n="23"/>2-Amino-1 ,3-propanediol (5.Og, 54.9mmol) was dissolved in dry THF (175ml) and triethylamine (7.7ml) added. The solution was cooled in an ice-bath and di-te/f- butylcarbonate (11.98g, 54.9mmol) added in portions over 15mins. The solution was allowed to warm to ambient temperature and stirred for 90mins. The solvent was evaporated and water (250ml) added and the product extracted into ethyl acetate (4 x 125ml). The combined organics were washed with brine, dried over magnesium sulphate, filtered and evaporated. The product was isolated by recrystallization from hot ethyl acetate-petrol (1 :3) to give shiny flakes 5.18g (49% yield).The structure was confirmed by 1H NMR (300MHz , CDCI3): 1.44 (s, 9H), 3.08- 3.17 (m, 1 H), 3.61 - 3.84 (m, 4H). |
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