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Surveying the scope of aromatic decarboxylations catalyzed by prenylated-flavin dependent enzymes
Anushree Mondal ; Pronay Roy ; Jaclyn Carrannatto , et al. Faraday Discuss.,2024,252,208-222. DOI: 10.1039/D4FD00006D PubMed ID: 38837123
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Abstract: The prenylated-flavin mononucleotide-dependent decarboxylases (also known as UbiD-like enzymes) are the most recently discovered family of decarboxylases. The modified flavin facilitates the decarboxylation of unsaturated carboxylic acids through a novel mechanism involving 1,3-dipolar cyclo-addition chemistry. UbiD-like enzymes have attracted considerable interest for biocatalysis applications due to their ability to catalyse (de)carboxylation reactions on a broad range of aromatic substrates at otherwise unreactive carbon centres. There are now ∼35[thin space (1/6-em)]000 protein sequences annotated as hypothetical UbiD-like enzymes. Sequence similarity network analyses of the UbiD protein family suggests that there are likely dozens of distinct decarboxylase enzymes represented within this family. Furthermore, many of the enzymes so far characterized can decarboxylate a broad range of substrates. Here we describe a strategy to identify potential substrates of UbiD-like enzymes based on detecting enzyme-catalysed solvent deuterium exchange into potential substrates. Using ferulic acid decarboxylase (FDC) as a model system, we tested a diverse range of aromatic and heterocyclic molecules for their ability to undergo enzyme-catalysed H/D exchange in deuterated buffer. We found that FDC catalyses H/D exchange, albeit at generally very low levels, into a wide range of small, aromatic molecules that have little resemblance to its physiological substrate. In contrast, the sub-set of aromatic carboxylic acids that are substrates for FDC-catalysed decarboxylation is much smaller. We discuss the implications of these findings for screening uncharacterized UbiD-like enzymes for novel (de)carboxylase activity.
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CAS No. : | 59-67-6 | MDL No. : | MFCD00006391 |
Formula : | C6H5NO2 | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | PVNIIMVLHYAWGP-UHFFFAOYSA-N |
M.W : | 123.11 | Pubchem ID : | 938 |
Synonyms : |
Nicotinic acid;Vitamin B3;NSC 169454
|
Chemical Name : | Nicotinic acid |
Signal Word: | Warning | Class: | N/A |
Precautionary Statements: | P264-P273-P280-P305+P351+P338-P337+P313-P501 | UN#: | N/A |
Hazard Statements: | H319-H413 | Packing Group: | N/A |
GHS Pictogram: |
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* 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 |
---|---|---|
80% | With sulfuric acid; In benzene; for 8.0h;Reflux; | General procedure: To the solution of n-butyl alcohol (110 mL) andbenzene (30 mL) which contained compounds of I(0.2 mol), concentrated sulfuric acid (98percent, d = 1.84)was added and stirred. The mixture was heated toreflux with a water separator and stirred for 8 hours,then the excess n-butyl alcohol and benzene wasdistillated out, the residuum was pour into ice water(150 mL) and neutralized to pH = 7?8 with saturatedsodium carbonate solution. The water solution wasextracted with isopropyl ether (3 × 100 mL). Thecombined extract solution was dried overnight byanhydrous magnesium sulfate and filtered. The filtratewas distillated out first the isopropyl ether thendistillated out the ester of II under vacuum. |
With NaOH; In toluene; | Example 3Preparation of Butyl Nicotinate in a Pressure Reactorn-Butanol (177.6 g, 2.4 mol), nicotinic Acid (98.4 g, 0.8 mol) and toluene (45.0 g) were charged to a 450 ml pressure reactor kettle and equipped with mechanical stir, a pressure take-out trap, and a thermocouple.The reactor was sparged with nitrogen and heated to 116° C., sealed, then heated to 200° C. and held for 6 hours.The mixture was then removed from the reaction kettle and volatiles removed under vacuum on a rotary evaporator at 60° C.The product was then purified by combining it with 50.0 g toluene and 60.1 g 4.4percent NaOH solution in a 500 mL separatory funnel.The organic layer was then separated, dried over 5 g MgSO4 and solvents removed under vacuum on a rotary evaporator at 60° C. to yield the desired product. | |
With sulfuric acid; | Example 1Preparation of Butyl Nicotinate Using Sulfuric Acid CatalystNicotinic Acid (3.0 g, 24.4 mmol) and n-butanol (9.0 g, 122 mmol) were mixed together at room temperature in a 2-neck 25 mL round bottom flask equipped with a magnetic stir bar and reflux condenser under an atmosphere of N2.Sulfuric acid (3.59 g, 36.6 mmol) was added dropwise to the flask over a period of 30 min.Once the addition was complete, the reaction mixture was heated to 85° C. and held for 2 hours.The reaction mixture was allowed to cool and poured over ice.The resulting solution was neutralized with K2CO3 and extracted with EtOAc (2*75 mL).The organic layer was dried over MgSO4, filtered, and concentrated to yield a light yellow liquid. 1H NMR (500 MHz, CDCl3): 9.229 ppm (s), 8.774 ppm (d), 8.305 (d), 7.391 (t), 4.369 (t), 1.762 (m), 1.484 (m), 0.991 (t). IR: 2956.6, 1719.5, 1590.8, and 705.1 cm-1. |
In Hg; n-heptane; | Example 2Preparation of Butyl Nicotinate Using Recyclable Alkylbenzene Sulfonic Acid CatalystNicotinic Acid (24.6 g, 0.2 mol), n-butanol (100.0 g, 1.33 mol) and heptane (20.1 g) were charged to a 500 mL reaction kettle and equipped with mechanical stir, a Dean-Stark trap, and thermocouple.The mixture was stirred at 300 rpm under nitrogen atmosphere and alkylbenzenesulfonic acid (480 mw, 120 g, 0.25 mol) was added dropwise through an addition funnel over 2 hours.The mixture was heated to 115° C. and held for 3 hours.A second portion of Nicotinic Acid (24.6 g, 0.2 mol) was added through a powder funnel and the temperature was increased to 150° C. and vacuum was applied to -29.5 in Hg and held for 1 hour.The distillate was then taken and solvents removed under vacuum on a rotary evaporator to yield the desired product.This process was repeated 2 additional times using the same Alkylbenzenesulfonic acid. | |
In toluene; | Example 16Preparation of Butyl Nicotinate in a Pressure Reactor without Aqueous ExtractionN-butanol (133.2 g, 1.8 mol), nicotinic acid (73.8 g, 0.6 mol) and toluene (45.0 g) were charged to a 450 mL pressure reactor kettle equipped with mechanical stir, a pressure take-out trap, and a thermocouple.The reactor was sparged with nitrogen and heated to 116° C., sealed, then heated to 220° C. and held for 6 hours.The mixture was then removed from the reaction kettle and volatiles removed under vacuum on a rotary evaporator at 60° C.The product was then filtered through celite on a Buchner funnel. 103.4 g product was obtained. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Compounds 41-70 were part of a parallel set prepared in library plate format according to General Procedure L, outlined below. ; L. General Procedure for Plate Preparation-Amide Formation XXI: Resin bound deprotected biarylphenol XVII (prepared from intermediate XII, boronates XIVd and XIVe, following general procedures D-F) was distributed into a 96 well plate, 10 mg of resin (0.013 mmol) per well. To the resin 400 mul of dichloromethane was added, followed by 100 mul of DIEA, followed by 0.13 mmol (10 equiv) of heterocyclic carboxylic acid XXa-XXn was added followed by 61 mg (0.13 mmol, 10 equiv) of PyBrop. The plate was shaken at room temperature for 24 hours, then drained and washed with dichloromethane, methanol/dichloromethane, dimethylformamide, methanol/dichloromethane and dichloromethane. The compounds were cleaved with TFA/dichloromethane (600 mul, 1:1) into a 96 deep well plate and submitted for testing without further purification. (Mass spec results obtained are shown in Table 4). Carboxylic Acids Het-COOH XX: |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
58.5%; 65.4% | With thionyl chloride; triethylamine; In toluene; | EXAMPLE 5 A mixture of 2.9 g (0.18 moles) of <strong>[1198-97-6]4-phenylpyrrolidin-2-one</strong> and nicotinoyl acid chloride, synthesised from 2.52 g (0.02 moles) of nicotinic acid and SOCl2, and 3.6 ml (0.04 moles) triethylamine in 15 ml toluene is heated for 9 hours at 100 C. to 110 C. and the precipitate is filtered off, washed with benzene and water and dried. N-nicotinoyl-<strong>[1198-97-6]4-phenyl-pyrrolidin-2-one</strong> (Substance No. 8), melting at 146 C.-147 C. (benzene), is obtained in a yield of 3.1 g, which corresponds to 58.5% of the theoretical yield of the compound having the empirical formula C16 H14 N2 O2. IR (KBr): 1746 (C=O), 1617 (C=O) N-(4-chlorobenzoyl)-<strong>[1198-97-6]4-phenyl-pyrrolidin-2-one</strong> (Substance No. 9), which melts at 157 C.-158 C. (benzene) was obtained similarly. The yield was 65.4% of the theoretical yield of the compound having the empirical formula C17 H14 NO2 Cl. IR (KBr): 1746 (C=O), 1617 (C=O) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | With N-ethyl-N,N-diisopropylamine; HATU;dmap; In N,N-dimethyl-formamide; at 0 - 20℃; for 2.16667h; | Example 15; 238 Part A: Compound 230 was prepared via the synthetic method described in Example14 (Part B). To a solution of nicotinic acid (0.23 g, 1.90 mmol) in DMF (10 ml_) was added compound 230 (0.46 g, 2.28mmol) and diisopropylethylamine (1.00 ml_, 5.70 mmol). The reaction mixture was stirred at room temperature for 10 minutes, cooled to O0C (ice-bath) and then added HATU (0.87 g, 2.28 mmol) and catalytic DMAP. The reaction mixture was allowed to warm to room temperature, stirred at room temperature for 2 hours. The reaction mixture was diluted with ethyl acetate and washed with 0.1 N NaOH (x1 ), water (x2), 0.1 N HCI (x1 ) and brine, dried over anh sodium sulfate and concentrated. Purification by column chromatography (Sitheta2, 10% MeOH / DCM) afforded compound 236 as a beige solid 0.60 g (100%). 1H NMR (400 MHz, DMSO-de) delta 9.73 (s, 1 H), 9.15 (d, 1 H), 8.73 (m, 1 H), 8.3 )m, 1 H), 7.55 (m, 1 H), 7.03 (d, 1 H), 6.69 (m, 2H), 2.78 (s, 3H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With phosphorus pentachloride; at 175℃; under 18751.9 - 30003 Torr; for 96h;Autoclave; | EXAMPLE 5 Conversion of Nicotinic acid to 2,3-dichloro-5-(trichloromethyl)pyridine. Using a similar setup as described in example 1, a series of experiments were carried out with 4 molar eq. of PCI5 at various temperatures and a pressure reaching between 25 and 40 bar after completion. Results are provided in table 2. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With phosphorus pentachloride; at 185℃; under 18751.9 - 30003 Torr; for 72h;Autoclave; | EXAMPLE 5 Conversion of Nicotinic acid to 2,3-dichloro-5-(trichloromethyl)pyridine. Using a similar setup as described in example 1, a series of experiments were carried out with 4 molar eq. of PCI5 at various temperatures and a pressure reaching between 25 and 40 bar after completion. Results are provided in table 2. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With phosphorus pentachloride; at 185℃; under 18751.9 - 30003 Torr; for 64h;Autoclave; | EXAMPLE 6 Conversion of Nicotinic acid to 2,3-dichloro-5-(trichloromethyl)pyridine. Using a similar setup as described in example 1, a series of experiments were carried out using various amounts of PCI5, at a temperature set at 210C, and at pressure reaching between 25 and 40 bar after completion. Results in accordance with the below table 3. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
75% | With chlorine; phosphorus trichloride; at 120 - 180℃; under 2250.23 - 12001.2 Torr;Autoclave; | EXAMPLE 10 Conversion of Nicotinic acid to 2,3-dichloro-5-(trichloromethyl)pyridine. Nicotinic acid (50 g, 0.4 mole) and phosphorous trichloride (223 g, 1.6 mole) were added to an 0.5 L jacketed autoclave, connected to a cooling- heating circulator. The temperature of the reaction mixture was adjusted to 120 C and chlorine gas (115 g, 1.6 mole) was added to head space from a pressure bottle. During addition of chlorine was the temperature maintained between 120 C and 140 C with cooling circulation on the jacket. After addition of chlorine gas is the pressure in the autoclave around 3 bar. The temperature is increased to 180 C (will be preferred to increase to 210 C, but this was not possible in the current setup) and kept there for 144 hours (210 C will finish reaction in 16 hours). During the reaction HCl(g) was removed through a scrubber periodically to keep pressure between 12 and 16 bar. The autoclave was then cooled to 25 C and ventilated to a Caustic Lye scrubber. The resulting solution was heated to reflux to recover phosphorous trichloride by distillation. The autoclave was closed again and chlorine gas (50 g, 0.5 mole) was added at room temperature. The resulting mixture was heated to 130 C and pressure was kept below 15 bar by removing HCl(g) above a condenser to a caustic lye scrubber. When pressure becomes stable (typically after 2 - 4 hours), the reaction is considered completed and the autoclave cooled down. If analysis shows otherwise, the final chlorination procedure can be repeated. The reaction mixture was then transferred to a round bottomed flask and phosphoryl chloride was removed by distillation. In case there is any solid PC15 in the reactor, it can be converted to phosphoryl chloride with a few drops of water and transferred together with the main reaction mixture. Upon distillation of phosphoryl chloride - the crude product was obtained by addition to ice cold water, stirred for 10 minutes and allowed to stand for separation for 1 hours at 25 C. The lower organic phase is separated from the acidic water phase and the product hereafter distilled to give 80 g of 2,3-dichloro-5-(trichloromethyl)pyridine with a purity of 96% (75% yield). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
33%Chromat.; 60%Chromat. | With phosphorus pentachloride; at 210℃; under 1500.15 - 27752.8 Torr; for 14h;Autoclave; | EXAMPLE 7 Conversion of Nicotinic acid to a mixture of 2-chloro-5- (trichloromethyl)pyridine and 2,3-dichloro-5-(trichloromethyl)pyridine. To a 250 ml Berghof autoclave with PTFE lining was added Nicotinic acid (20g, 162 mmole) and phosphorous pentachloride (139 g, 668 mmole). The autoclave was closed and heated to 210 C for 14 hours. During the heating an exotherm was observed around a temperature of 130 C bringing the temperature to 190 C and a pressure increase from 2 bar to 8 bar within 2 minutes. The heating was continued to 210 C. After the 14 hours the pressure had increased to 37 Bar. The autoclave was cooled to room temperature, ventilated to a scrubber, opened and quantified by GC indicating a yield of 2- chloro-5-(trichloromethyl)pyridine of 33% compared to the Nicotinic acid starting material and a yield of 2,3-dichloro-5-(trichloromethyl)pyridine 60%. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
General procedure: To a solution of 3a (1 g) in ethanol was added Pd/C (5%, 0.1 g) and the mixture was stirred for 24 hrs at room temperature in a hydrogen atmosphere under atmospheric pressure. Insoluble matters were removed using Celite, and the filtrate was concentrated in vacuo to give the desired product 4a (0.76 g) as a yellow solid. To a solution of carboxylic acid (1 equiv) in CH2Cl2 (15 mL) at 0 C was added DMAP (1 equiv) and EDCI (1 equiv). The reaction mixture was stirred at 0 C for 45 minutes. At this time 4a (1 equiv) was added and the mixture was warmed to room temperature and stirred overnight. The resulting mixture was concentrated in vacuo, partitioned between 1.0 M HCl (20 ml) and ethyl acetate (3×20 mL). The combined organic layers were washed with brine (2 × 15 ml), dried over Na2SO4, filtered and concentrated in vacuo. The crude residue was purified by silica gel chromatograph using a mixture of petroleum ether/ethyl acetate (20 : 5, v/v) as eluent to afford the product as a white solid. To a solution of the obtained solid (1 equiv) in 2:3:1 THF/MeOH/H2O (18 ml) was added LiOH·H2O (1.5 equiv). After stirring at room temperature for 4 h, the volatiles were removed under reduced pressure. The residue was acidified with 1N hydrochloric acid solution, and then filtered and the filter cake was washed with 5 mL of water, dried in vacuum to afford a white powder. Recrystallization from 75% EtOH gave the desired compounds 2-17 as white solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
6.85 g | Weigh 6.10g of <strong>[436-77-1]fangchinoline</strong>, 2.26g of 2-methoxy-4-trifluoromethylbenzyl chloride, dissolved in 100mL of n-butanol in a 500mL three-necked flask, add 10mL of triethylamine, and heat under mixing and stirring. To the boiling, and stirring reaction for 8h, TLC detection of all reactions of anti-ninoline, adding 30% nicotinic acid to pH=7.1, separating the solvent n-butanol by heating under reduced pressure, 200g of alumina column chromatography, two Methyl chloride-methanol (5:1) elution, TLC tracking reaction and product separation and purification process, collecting and combining product fractions, and distilling off the solvent at 60 C with a rotary evaporator to obtain a product of light yellow powder 6.85 g . |