Synthesis of Novel Pyrazine-Substituted 1H-Pyrrole-2-carboxamides and Related Tethered Heterocycles

Abstract

As part of a drug discovery program, 4-pyrazin-2-yl-1H-pyrrole-2-carboxamides were accessed along with a number of bicyclic analogues. Routes to these compounds were largely absent from the scientific literature. The synthesis of a 4-(pyrazin-2-yl)-1H-pyrrole-2-carboxamide and several fused bicyclic analogues all using standard procedures (S_NAr, borylation, C–C cross couplings, hydrolysis, amide bond formation, cyclisation, halogenation, and alkylation) from readily available starting materials is reported. The synthetic sequences range from 4–12 steps per final compound, with yields of isolated intermediates ranging from 20 to ∼100%.

Monocyclic and fused bicyclic nitrogen heterocycles feature extensively in drug molecules.[1] As part of an internal drug discovery project targeting the extracellular-signal-regulated kinase (ERK) pathway, we wished to synthesise 4-(pyrazin-2-yl)-1H-pyrrole-2-carboxamides and several fused bicyclic analogues to explore key interactions in the target protein. We were surprised to find these structural motifs were absent from the scientific literature, with only N-methylated pyrroles with 4-pyrazine connectivity being known.[2] Herein we report the synthesis of one specific 4-pyrazin-2-yl-1H-pyrrole-2-carboxamide derivative (Scheme [1]) and several of the aforementioned fused bicyclic analogues.

We constructed compound 1 from commercially available reagents using common transformations known in the literature (Scheme [1]). An S_NAr reaction on 2,6-dichloropyrazine (1a) with morpholine (1b) afforded 4-(6-chloropyrazin-2-yl)morpholine (1c). Subsequent Suzuki–Miyaura[3] coupling with boronic ester 1e, which was synthesised from borylation of commercial 1-tert-butyl 2-methyl 1H-pyrrole-1,2-dicarboxylate (1d), gave ester 1f. Hydrolysis of the ester with lithium hydroxide also gave an unexpected in situ tert-butyloxycarbonyl (Boc) deprotection affording compound 1g in excellent yield. We postulated that as the Boc group is present on an activated pyrrole amine it is susceptible to cleavage under strong basic conditions.[4] A final amide coupling using 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate (HATU) gave the desired 4-pyrazin-2-yl-1H-pyrrole-2-carboxamide 1 in moderate yield. Utilising this synthetic route, we were able to rapidly synthesise over 400 compounds, varying both the amide and morpholine substitution.

With these 4-pyrazin-2-yl-1H-pyrrole-2-carboxamide compounds in hand we turned our attention to 5,6-fused analogues. The unsubstituted bicyclic cores we were interested in synthesising and their subsequent pyridine analogues are reported in the literature,[5] [6] [7] [8] but again we found that there was no precedent for the required specific pyrazine-substituted compounds. 22453271014378

We initially looked at the synthesis of a 1,6-dihydropyrrolo[2,3-c]pyridin-7-one derivative (Scheme [2], compound 2). A reductive amination between commercially available benzaldehyde and 2,2-dimethoxyethanamine (2a) afforded N-benzyl-2,2-dimethoxyethanamine (2b) in low yield. This was then coupled with 4-bromo-1H-pyrrole-2-carboxylic acid to give carboxamide 2c. An acid-promoted cyclisation gave the functionalised tethered bicycle 2d in a moderate yield, which was then Boc protected to afford compound 2e. The following three steps were then telescoped; borylation with bis(pinacolato)diboron to afford crude boronic ester 2f; Suzuki–Miyaura coupling with intermediate 1c followed by Boc deprotection to afford the desired tethered pyrrolo[2,3-c]pyridin-7(6H)-one 2 in reasonable yield. We were then able to methylate the pyrrole nitrogen, affording compound 3 as an additional final product. We were interested in introducing a variety of benzyl groups and so devised a route where this functionality could be introduced later in the synthesis. 7-Methoxy-1H-pyrrolo[2,3-c]pyridine (4a) was protected using a 2-(trimethylsilyl)ethoxymethyl (SEM) group to afford compound 4b. Subsequent bromination with N-bromosucinimide (NBS) generated compound 4c in excellent yield. A trimethylsilyl chloride (TMSCl) demethylation gave the fused pyridinone 4d, which was then alkylated with 1-(bromomethyl)-3-chlorobenzene to afford chloro intermediate 4e. The following three steps were again telescoped as for compound 2; borylation with bis(pinacolato)diboron gave intermediate 4f, which was used crude in a Suzuki–Miyaura coupling with 1c to give compound 4g. A TFA-mediated SEM deprotection afforded compound 4 in good yield.

We naturally then looked at the synthesis of a pyrrolo[3,2-d]pyrimidin-4(5H)-one analogue (Scheme [3], compound 5), in order to be able to add an extra nitrogen into the tethered ring system. Ethyl 3-amino-1H-pyrrole-2-carboxylate hydrochloride (5a) was converted to the free base and then brominated using NBS generating ethyl 3-amino-4-bromo-1H-pyrrole-2-carboxylate (5b). This compound then underwent cyclisation with formamidine acetate to afford the pyrimidine-fused bicycle 5c in excellent yield. Boc protection was then followed by benzyl alkylation of the free NH to afford 5e. We originally sought to synthesise the boronic ester and so both a palladium-catalysed borylation of 5e and an iridium-mediated borylation on the des-bromo derivative were attempted, but unfortunately neither yielded the desired pinacol ester intermediate. Borylation of the pyrazine was not attempted by our group, although since our research was conducted an efficient protocol for the synthesis of 2-borylpyrazines has been developed.[9] These findings rendered a Suzuki–Miyaura coupling with 1c unviable and so we switched to a Stille coupling[10] with stannane 5h, prepared from 4-(6-bromopyrazin-2-yl)morpholine (5g), to afford 5i, albeit in a low yield. Deprotection delivered final compound 5.

We also investigated moving the pyrrole nitrogen to link directly to the pyrazine (Scheme [4]). The unsubstituted bicycle was known in the literature[11] as well as alkyl[12] and heterocycle[13] analogues including pyridine,[13a] [b] but our desired connectivity to the pyrazine has not been reported. We were pleased to generate this compound in only 3 steps starting with an S_NAr between 4-chloro-1H-pyrrolo[3,2-c]pyridine (6a) and intermediate 1c to afford 6b in moderate yield. Acidolysis of the chloro functional group using sodium acetate and acetic acid gave the pyridinone 6c, which was N-alkylated with benzyl bromide to afford compound 6.

Compounds containing a bridgehead nitrogen were also of interest to us (Scheme [5]), but again the unsubstituted bicycle,[14] alkyl,[15] and heterocycle[15a] [16] analogues including pyridine[17] had been reported, but not with a pyrazine motif attached. The six-step route was initiated with a bromination of commercial 1H-pyrrole-2-carboxylic acid (7a) to give compound 7b. The next three steps were telescoped; an amide coupling of 7b with (1,3-dioxolan-2-yl)methanamine afforded 7c; a p-toluenesulfonic acid-promoted cyclisation then gave compound 7d, which was subsequently dehydrated in a reasonable yield using methanesulfonic acid to afford 6-bromopyrrolo[1,2-a]pyrazin-1(2H)-one (7e). Alkylation with benzyl bromide gave compound 7f in good yield, which was then coupled with stannane 5h (described previously) to afford target compound 7.

The synthesis of fused imidazole 8 (Scheme [6]) was also of interest to the project. The unsubstituted bicycle is described in only one reference in the literature,[18] alkyl and heterocycle analogues are known,[18] [19] but this particular pyrazine heterocycle has not been exemplified. An amide coupling between commercial reagents 6-morpholinopyrazine-2-carboxylic acid (8a) and the dihydrochloride salt of amine 8b afforded N-[(3-chloropyrazin-2-yl)methyl]-6-morpholinopyrazine-2-carboxamide (8c) in quantitative yield. Cyclisation using phosphorus(V) oxychloride and catalytic DMF afforded the imidazopyrazine system 8d, which was then manipulated via acidolysis to give the imidazo­pyrazinone 8e. Lastly, N-benzylation with benzyl bromide gave compound 8 in good yield.

To compliment our 5,6-fused systems, we were keen to access the 5,5-fused system exemplified by compound 9 (Scheme [7]). This particular 5,5-system had been described with various functional group substitutions,[20] but as before no report of pyrazine functionality. We previously reported the synthesis of compound 9a [21] and were able to subsequently elaborate on this synthesis to afford compound 9. First, compound 9a was alkylated with 4-(bromomethyl)-1,2-dichlorobenzene to give 9b. An iridium-mediated borylation generated a regiochemical mixture of pinacol esters, in both the 2- and 3-positions on the pyrrole ring, this was in favour of the desired isomer 9c (ratio 2:1, respectively). This mixture was carried forward crude into the Suzuki–Miyaura coupling with 4-(6-chloropyrazin-2-yl)morpholine (1c), at which stage we were pleased to find that the regioisomers could be separated to afford the desired coupled product 9d. Boc deprotection with TFA then afforded the 5,5-dihydropyrrolo[3,4-b]pyrrol-6(1H)-one system, compound 9.

In conclusion, a variety of novel pyrazine-substituted 1H-pyrrole-2-carboxamides and structurally related tethered heterocycles have been prepared as part of a drug discovery project. We have designed, developed, and successfully executed routes to these novel structural motifs.

All materials were sourced from commercial suppliers and used as provided. Reaction progress was monitored by Waters Aquity UPLC with Waters 3100 Mass detection or TLC using glass plates pre-coated with 0.25 mm 300–400 mesh silica gel impregnated with a fluorescent indicator (254 nm). Visualisation was by exposure to UV light. Flash column chromatography was performed using pre-loaded Silicycle columns containing silica gel (60Å pore size, standard grade) and an Isco Combi-Flash Companion. Reverse phase chromatography was performed using pre-loaded RediSep Rf cartridges containing C18 silica and a Teledyne Isco Combi-Flash Rf. Details of preparative HPLC purification are contained within the experimental information where relevant. The high-resolution mass spec was obtained using a Thermo LTQ-FT/Accela/CTC/PDA with Acquity 50 × 2.1 C18 CSH 1.7 μm columns at 40 °C. NMR spectra were recorded on a Bruker 300, 400, or 500 MHz instrument at RT, unless otherwise stated, using DMSO-d ₆, CDCl₃ or CD₃OD and are reported relative to a protiated solvent signal or TMS.

Synthesis of N-Benzyl-4-(6-morpholinopyrazin-2-yl)-1H-pyrrole-2-carboxamide (1)

4-(6-Chloropyrazin-2-yl)morpholine (1c)[22]

Morpholine (1b; 6.45 mL, 73.76 mmol) was added to a mixture of 2,6-dichloropyrazine (1a; 9.99 g, 67.06 mmol) and Et₃N (11.22 mL, 80.47 mmol) in MeCN (200 mL) at RT. The reaction was then warmed to reflux for 4 h. The solvents were removed and the residue was dissolved in DCM (200 mL), which was then washed with sat. aq NH₄Cl (200 mL). The organic layers were passed through a phase separating cartridge and concentrated in vacuo. The resulting solid was triturated with Et₂O, filtered, and dried; yield: 11.81 g (88%); white solid (Lit.[23] mp 150–152 °C).

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.46–3.60 (m, 4 H), 3.64–3.76 (m, 4 H), 7.89 (s, 1 H), 8.28 (d, J = 0.5 Hz, 1 H).

MS (ES+): m/z = 200 [M + H]⁺.

1-tert-Butyl 2-Methyl 4-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrole-1,2-dicarboxylate (1e)[23]

Bis(pinacolato)diboron (10.65 g, 41.96 mmol), (1,5-cyclooctadiene)(methoxy)iridium(I) dimer (0.424 g, 0.64 mmol) and 4,4′-di-tert-butyl-2,2′-bipyridine (BBBPY, 0.354 g, 1.32 mmol) were placed in a 250 mL three-necked flask, which was purged with N₂. Degassed tert-butyl methyl ether (MTBE) (100 mL) was added and the mixture was stirred until a clear brown solution was obtained. 1-tert-Butyl 2-methyl 1H-pyrrole-1,2-dicarboxylate[24] (9.00 g, 39.96 mmol) was added and the mixture stirred at 65 °C for 2 h. The reaction was cooled to RT and concentrated in vacuo. The crude product was purified by flash silica gel chromatography with DCM as eluent. Fractions were evaporated to afford a liquid. Heptane (60 mL) was added and the solution was left stirring overnight. The resultant precipitate was filtered and washed with 5% DCM in heptane; yield: 9.60 g (68%); off-white solid (Lit.[23] mp 133–135 °C).

¹H NMR (500 MHz, CDCl₃): δ = 1.31 (s, 12 H), 1.58 (s, 9 H), 3.82 (s, 3 H), 7.12 (d, J = 1.7 Hz, 1 H), 7.68 (d, J = 1.7 Hz, 1 H).

MS (ES+): m/z = 297 ([M + H]⁺ – OtBu).

1-tert-Butyl 2-Methyl 4-(6-Morpholinopyrazin-2-yl)-1H-pyrrole-1,2-dicarboxylate (1f)

4-(6-Chloropyrazin-2-yl)morpholine (1c; 5.50 g, 27.55 mmol), Pd(PPh₃)₄ (2.55 g, 2.20 mmol), and 1-tert-butyl 2-methyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrole-1,2-dicarboxylate (1e; 9.68 g, 27.55 mmol) were dissolved in degassed DME (137 mL). To this solution was added aq 2 M Na₂CO₃ (27.5 mL, 55.10 mmol) and the reaction mixture was heated at 85 °C for 1 h. The mixture was cooled to RT before DCM (400 mL) was added and the mixture washed with H₂O (400 mL). The layers were separated and the organic layer was passed through a phase separation cartridge and concentrated in vacuo to give a brown gum. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 50% of EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 8.50 g (79%); brown oil which solidified on standing.

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.56 (s, 9 H), 3.54–3.64 (m, 4 H), 3.7–3.78 (m, 4 H), 3.82 (s, 3 H), 7.44 (d, J = 1.8 Hz, 1 H), 8.09 (d, J = 1.8 Hz, 1 H), 8.18 (s, 1 H), 8.38 (s, 1 H).

MS (ES+): m/z = 389 [M + H]⁺.

4-(6-Morpholinopyrazin-2-yl)-1H-pyrrole-2-carboxylic Acid (1g)

LiOH·H₂O (1.73 g, 41.19 mmol) was added to a stirred solution of 1-tert-butyl 2-methyl 4-(6-morpholinopyrazin-2-yl)-1H-pyrrole-1,2-dicarboxylate (1f; 3.20 g, 8.24 mmol) in a mixture of THF (65 mL) and H₂O (16 mL) and the reaction mixture heated to 60 °C for 16 h. The mixture was purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded. The column was washed with MeOH before the desired product was eluted from the column using 1 M NH₃ in MeOH and pure fractions were evaporated to dryness; yield: 2.20 g (97%); yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.41–3.68 (m, 4 H), 3.68–3.91 (m, 5 H), 7.10 (d, J = 1.6 Hz, 1 H), 7.49 (d, J = 1.7 Hz, 1 H), 8.01 (s, 1 H), 8.23 (s, 1 H), 11.5 (br s, 1 H).

MS (ES+): m/z = 275 [M + H]⁺.

N-Benzyl-4-(6-morpholinopyrazin-2-yl)-1H-pyrrole-2-carbox­amide (1)

HATU (0.865 g, 2.28 mmol) was added to a stirred mixture of 4-(6-morpholinopyrazin-2-yl)-1H-pyrrole-2-carboxylic acid (1g; 0.416 mg, 1.52 mmol) and DIPEA (1.32 mL, 7.58 mmol) in DMF (5.24 mL) at RT under N₂ and the reaction mixture stirred for 30 min. Phenylmethanamine (0.33 mL, 3.03 mmol) was then added and the mixture stirred for 3 h. The reaction was incomplete and additional amounts of phenylmethanamine (0.33 mL, 3.03 mmol), DIPEA (1.32 mL, 7.58 mmol), DMF (5.24 mL), and finally HATU (0.865 mg, 2.28 mmol) were added and the mixture was stirred at 20 °C for a further 2 h. The reaction was quenched with a 50:50 mixture of H₂O and 28–30% NH₄OH (50 mL) and the resultant solution stirred for 15 min. A precipitate formed was collected by filtration and washed with H₂O. The solid was dried in the vacuum oven at 50 °C overnight to afford a cream solid. The solid was triturated and sonicated with MeCN (25 mL), before being filtered and washed with further MeCN. The resulting solid was dried under high vacuum; yield: 0.179 g (33%); beige solid.

¹H NMR (500 MHz, DMSO-d ₆, 27 °C): δ = 3.55–3.61 (m, 4 H), 3.71–3.77 (m, 4 H), 4.46 (d, J = 6.0 Hz, 2 H), 7.25 (m, 1 H), 7.28–7.37 (m, 4 H), 7.41 (s/br t, 1 H), 7.58–7.60 (m, 1 H), 8.02 (s, 1 H), 8.20 (s, 1 H), 8.72 (t, J = 6.0 Hz, 1 H, NH), 11.86 (s, 1 H, NH).

¹³C NMR (126 MHz, DMSO-d ₆, 27 °C): δ = 41.89, 44.25 (2 C), 65.82 (2 C), 108.25, 121.10, 122.29, 126.67, 126.80, 127.20 (2 C), 127.33, 128.21 (2 C), 128.66, 139.83, 146.05, 153.88, 160.31.

MS (ES+): m/z = 364 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₀H₂₁N₅O₂: 364.17680; found: 364.17725.

Synthesis of 6-Benzyl-3-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (2)

N-Benzyl-2,2-dimethoxyethanamine (2b)[25]

2,2-Dimethoxyethanamine (2a; 3.11 mL, 28.53 mmol) and benzaldehyde (2.90 mL, 28.53 mmol) were stirred in MeOH (50 mL) at 0 °C for 30 min. NaBH₄ (2.159 g, 57.07 mmol) was then added portionwise over 15 min and the reaction mixture allowed to warm to RT and stirred for a further 16 h. The solvents were removed in vacuo. The residue was then dissolved in EtOAc (100 mL) and washed with H₂O (100 mL). The aqueous phase was re-extracted with EtOAc (100 mL), and the combined organics washed with brine (100 mL), dried (Na₂SO­₄), filtered and evaporated to give a gum. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 1.601 g (29%) (Lit.[25] bp 102 °C/760 Torr).

¹H NMR (500 MHz, CDCl₃): δ = 2.75 (d, J = 5.5 Hz, 2 H), 3.37 (s, 6 H), 3.81 (s, 2 H), 4.49 (t, J = 5.5 Hz, 1 H), 7.03–7.44 (m, 5 H). One exchangeable H not seen.

Not visible on LCMS.

N-Benzyl-4-bromo-N-(2,2-dimethoxyethyl)-1H-pyrrole-2-carboxamide (2c)

DIPEA (4.28 mL, 24.58 mmol) was added to a stirred solution of 4-bromo-1H-pyrrole-2-carboxylic acid (1.56 g, 8.19 mmol), N-benzyl-2,2-dimethoxyethanamine (2b; 1.60 g, 8.19 mmol), and HATU (4.05 g, 10.65 mmol) in DMF (20 mL) and the reaction mixture stirred at 20 °C for 16 h. DCM (100 mL) was added and the mixture washed with H₂O (100 mL). The layers were separated, and the organic layer was passed through a phase separating cartridge and concentrated in vacuo to give a beige solid. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 50% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 1.33 g (44%); colourless liquid.

¹H NMR (500 MHz, CDCl₃): δ = 3.40 (s, 6 H), 3.56 (d, J = 19.7 Hz, 2 H), 4.68 (s, 1 H), 4.91 (d, J = 45.0 Hz, 2 H), 6.43 (s, 1 H), 6.91 (dd, J = 1.4, 3.0 Hz, 1 H), 7.11–7.47 (m, 5 H), 9.80 (s, 1 H).

MS (ES+): m/z = 187 [M + H]⁺.

6-Benzyl-3-bromo-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (2d)

N-Benzyl-4-bromo-N-(2,2-dimethoxyethyl)-1H-pyrrole-2-carboxamide (2c; 1.33 g, 3.62 mmol) was dissolved in TFA (20 mL) and the reaction mixture stirred at 90 °C for 16 h. The solvents were then removed in vacuo. The residue was diluted with DCM (100 mL) and washed sequentially with sat. aq NaHCO₃ (200 mL), H₂O (100 mL), and brine (125 mL). The organic layer was passed through a phase separating cartridge and concentrated under reduced pressure to give a dark grey solid. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 50% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 0.532 g (49%); yellow waxy solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 5.20 (d, J = 6.5 Hz, 2 H), 6.39 (dd, J = 0.6, 7.1 Hz, 1 H), 7.09–7.43 (m, 6 H), 7.51 (d, J = 2.9 Hz, 1 H), 12.43 (s, 1 H).

MS (ES+): m/z = 305 [M + H]⁺.

tert-Butyl 6-Benzyl-3-bromo-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-1-carboxylate (2e)

NaH (60% in mineral oil; 0.21 g, 5.24 mmol) was added portionwise to a stirred suspension of 6-benzyl-3-bromo-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (2d; 0.53 g, 1.75 mmol) in MeCN (10 mL) at 0 °C over 15 min. Di-tert-butyl dicarbonate (0.763 g, 3.50 mmol) was then added and the reaction mixture allowed to warm to RT and stirred for a further 16 h. Sat. aq NH₄Cl (10 mL) was then added, the mixture diluted with H₂O (50 mL) and extracted with DCM (2 × 50 mL). The combined organics were passed through a phase separating cartridge and concentrated in vacuo to give a brown gum. The crude product was purified by flash silica gel chromatography (eluent: 0 to 25% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 0.604 g (86%); yellow gum.

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.55 (s, 9 H), 5.19 (d, J = 8.8 Hz, 2 H), 6.40 (d, J = 7.1 Hz, 1 H), 7.08–7.42 (m, 5 H), 7.66 (d, J = 7.1 Hz, 1 H), 7.97 (s, 1 H).

MS (ES+): m/z = 305 [M + H]⁺.

6-Benzyl-3-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (2)

Pd(dppf)Cl₂ (0.110 g, 0.15 mmol) was added to a degassed suspension of tert-butyl 6-benzyl-3-bromo-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-1-carboxylate (2e; 0.606 g, 1.50 mmol), bis(pinacolato)diboron (0.572 g, 2.25 mmol), and KOAc (0.295 g, 3.01 mmol) in 1,4-dioxane (10 mL) and the reaction mixture stirred at 90 °C for 16 h. The mixture was then cooled to RT and the solvents removed in vacuo. The residue was dissolved in DCM (200 mL) and washed sequentially with H₂O (200 mL) and brine (100 mL). The organic layer was dried by passing through a phase separating cartridge and concentrated in vacuo to give a dark brown gum. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 15% EtOAc in heptane). Fractions were evaporated to dryness to afford crude tert-butyl 6-benzyl-7-oxo-3-(4,4,5,5-tetramethyl-1,3,2-dioxa­borolan-2-yl)-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-1-carboxylate (2f); yield: 0.407 g (60%, ∼50% pure) as a dark yellow gum. Material used crude and not fully isolated.

MS (ES+): m/z = 395 [M + H]⁺.

4-(6-Chloropyrazin-2-yl)morpholine (1c; 0.118 g, 0.59 mmol), Pd(PPh₃)₄ (0.055 g, 0.05 mmol) and crude 2f (0.407 g, 0.89 mmol, ∼50% pure) were dissolved in degassed DME (5 mL). To this solution was added aq 2 M Na₂CO₃ (0.592 mL, 1.18 mmol) and the reaction mixture was heated at 85 °C for 1 h. The mixture was cooled to RT before DCM was added (50 mL) and the mixture washed with H₂O (50 mL). The layers were separated and the organic layer was passed through a phase separating cartridge before being concentrated in vacuo to give crude tert-butyl 6-benzyl-3-(6-morpholinopyrazin-2-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-1-carboxylate (2g) an orange gum; yield: 0.289 g (∼50% pure). Mixture of deprotected material and desired product. Material used crude and not fully isolated.

MS (ES+): m/z = 488 [M + H]⁺.

TFA (2 mL) was added to a stirred solution of crude 2g (0.289 g, 0.59 mmol, ∼50% pure) in DCM (5 mL). The reaction mixture was stirred for 2 h at RT before the crude mixture was partially purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded, eluted with MeOH before the desired product was eluted from the column using 1 M NH₃/MeOH. The basic fraction containing the desired product was evaporated to dryness to afford a yellow solid. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane followed by 10% MeOH in EtOAc). Pure fractions were evaporated to dryness to afford 2; yield 0.108 g (47%); pale yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.43–3.67 (m, 4 H), 3.67–3.86 (m, 4 H), 5.22 (s, 2 H), 7.19 (d, J = 7.2 Hz, 1 H), 7.23–7.38 (m, 6 H), 8.07 (d, J = 4.2 Hz, 2 H), 8.39 (s, 1 H), 12.45 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.58, 49.75, 65.79, 101.81, 114.81, 124.80, 126.84, 127.07, 127.27, 127.48, 127.78, 128.48, 129.54, 129.84, 138.21, 146.82, 154.08, 154.22.

MS (ES+): m/z = 388 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₂H₂₁N₅O₂: 388.1768; found: 388.17729.

6-Benzyl-1-methyl-3-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (3)

NaH (60% in mineral oil; 5.90 mg, 0.15 mmol) was added to a solution of 6-benzyl-3-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[2,3-c]pyridin-7(6H)-one (2; 52.0 mg, 0.13 mmol) in DMF (2 mL) at 0 °C, and the reaction mixture was allowed to warm to RT and stirred for a further 15 min. MeI (9.19 μL, 0.15 mmol) was then added and the mixture stirred for 90 min. The reaction was quenched with sat. aq NH₄Cl (3 mL), partitioned between DCM (50 mL) and H₂O (50 mL), and the organic layer collected. The aqueous layer was further extracted with DCM (50 mL). The combined organic layers were washed with brine, dried by passing through a phase separating cartridge and evaporated to dryness to afford crude product. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 35.0 mg (65%); pale yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.46–3.63 (m, 4 H), 3.68–3.83 (m, 4 H), 4.13 (s, 3 H), 5.17 (s, 2 H), 7.17 (d, J = 7.2 Hz, 1 H), 7.21–7.44 (m, 6 H), 8.08 (d, J = 3.7 Hz, 2 H), 8.29 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 35.93, 44.54, 49.84, 65.80, 101.53, 113.03, 123.52, 126.96, 127.28, 127.56, 128.48, 128.70, 129.29, 130.43, 132.00, 138.16, 146.43, 154.08, 154.84.

MS (ES+): m/z = 402 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₃H₂₃N₅O₂: 402.1925; found: 402.19409.

Synthesis of 6-(3-Chlorobenzyl)-3-(6-morpholinopyrazin-2-yl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4)

7-Methoxy-1-{[2-(trimethylsilyl)ethoxy]methyl}-1H-pyrrolo[2,3-c]pyridine (4b)

[2-(Chloromethoxy)ethyl]trimethylsilane (15.36 g, 92.13 mmol) was added dropwise to a solution of NaH (60% in mineral oil; 5.26 g, 131.61 mmol) and 7-methoxy-1H-pyrrolo[2,3-c]pyridine (4a;[26] 13 g, 87.74 mmol) in THF (200 mL) at 0 °C. The resulting mixture was warmed to RT over a period of 5 h. The mixture was quenched with sat. aq NH₄Cl (200 mL) and extracted with EtOAc (3 × 200 mL). The combined organic layers were dried (Na₂SO₄), filtered and evaporated to afford crude material. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 10% EtOAc in PE) and pure fractions were evaporated to dryness; yield: 23.00 g (94%); yellow oil.

¹H NMR (400 MHz, CDCl₃): δ = –0.07 (s, 9 H), 0.84–0.9 (m, 2 H), 3.48–3.54 (m, 2 H), 4.11 (s, 3 H), 5.75 (s, 2 H), 6.50 (d, J = 3.1 Hz, 1 H), 7.14 (d, J = 5.6 Hz, 1 H), 7.25 (d, J = 3.1 Hz, 1 H), 7.76 (d, J = 5.6 Hz, 1 H).

MS (ES+): m/z = 279 [M + H]⁺.

3-Bromo-7-methoxy-1-{[2-(trimethylsilyl)ethoxy]methyl}-1H-pyrrolo[2,3-c]pyridine (4c)

NBS (14.70 g, 82.61 mmol) was added portionwise to a solution of 7-methoxy-1-{[2-(trimethylsilyl)ethoxy]methyl}-1H-pyrrolo[2,3-c]pyridine (4b; 23 g, 82.61 mmol) in MeCN (200 mL). The resulting mixture was stirred at 0 °C for 4 h. The mixture was quenched with H₂O (200 mL) and extracted with EtOAc (2 × 300 mL). The combined organic layers were dried (Na₂SO₄), filtered and evaporated to afford an orange oil. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 10% EtOAc in PE) and pure fractions were evaporated to dryness; yield: 25 g (85%); orange liquid.

¹H NMR (400 MHz, CDCl₃): δ = –0.06 (s, 9 H), 0.85–0.91 (m, 2 H), 3.49–3.54 (m, 2 H), 4.11 (s, 3 H), 5.71 (s, 2 H), 7.09 (d, J = 5.6 Hz, 1 H), 7.28 (s, 1 H), 7.83 (d, J = 5.7 Hz, 1 H).

MS (ES+): m/z = 357/359 [M + H]⁺.

3-Bromo-1-{[2-(trimethylsilyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4d)

Trimethylchlorosilane (3.40 mL, 26.59 mmol) was added dropwise to a solution of 3-bromo-7-methoxy-1-{[2-(trimethylsilyl)ethoxy]methyl}-1H-pyrrolo[2,3-c]pyridine (4c; 5.0 g, 13.99 mmol) and NaI (3.99 g, 26.59 mmol) in MeCN (200 mL) at 25 °C under N₂. The resulting mixture was stirred at 25 °C for 12 h. This reaction was worked up together with another 6.0 g batch. The combined reaction mixtures were quenched with sat. aq NaHCO₃ (150 mL) and extracted with EtOAc (3 × 150 mL). The combined organic layers were dried (Na₂SO₄), filtered and evaporated to afford crude material. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 2% MeOH in DCM) and pure fractions were evaporated to dryness; yield: 8.00 g (combined batches 76%); pale yellow solid.

¹H NMR (300 MHz, DMSO-d ₆): δ = –0.09 (s, 9 H), 0.76–0.83 (m, 2 H), 3.48–3.55 (m, 2 H), 5.82 (s, 2 H), 6.30 (d, J = 6.7 Hz, 1 H), 6.99–7.06 (m, 1 H), 7.71 (s, 1 H), 11.24 (d, J = 4.8 Hz, 1 H).

MS (ES+): m/z = 344 [M + H]⁺.

3-Bromo-6-(3-chlorobenzyl)-1-{[2-(trimethylsilyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4e)

1-(Bromomethyl)-3-chlorobenzene (1.796 g, 8.74 mmol) was added to a solution of 3-bromo-1-{[2-(trimethylsilyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4d; 1.50 g, 4.37 mmol) and Cs₂CO₃ (4.27 g, 13.11 mmol) in DMF (15 mL) and heated to 80 °C for 20 h. This reaction mixture was combined with a second 1.50 g batch and worked up together. The combined reaction mixtures were diluted with EtOAc (300 mL) and washed sequentially with brine (100 mL) and H₂O (100 mL). The organic layer was dried (Na₂SO₄), filtered and evaporated to afford crude product. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 10% EtOAc in PE) and pure fractions were evaporated to dryness; yield: 4.00 g (combined batches 98%); colourless oil.

¹H NMR (400 MHz, CDCl₃): δ = –0.05 (s, 9 H), 0.88–0.94 (m, 2 H), 3.57–3.62 (m, 2 H), 5.18 (s, 2 H), 5.95 (s, 2 H), 6.46 (d, J = 7.1 Hz, 1 H), 7.01 (d, J = 7.1 Hz, 1 H), 7.12–7.16 (m, 1 H), 7.21–7.26 (m, 3 H), 7.29 (s, 1 H).

MS (ES+): m/z = 468 [M + H]⁺.

6-(3-Chlorobenzyl)-3-(6-morpholinopyrazin-2-yl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4)

PdCl₂[P(cy)₃]₂ (0.631 g, 0.85 mmol) was added to 3-bromo-6-(3-chlorobenzyl)-1-{[2-(trimethylsilyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4e; 4.0 g, 8.55 mmol), KOAc (1.678 g, 17.10 mmol), and bis(pinacolato)diboron (3.26 g, 12.82 mmol) in dimethylacetamide (50 mL) at 25 °C under N₂. The resulting mixture was stirred at 120 °C for 2 h. The mixture was quenched with H₂O (300 mL) and extracted with EtOAc (3 × 200 mL). The combined organic layers were dried (Na₂SO₄), filtered and evaporated to afford crude product. The crude product was partially purified by flash silica gel chromatography (eluent: gradient 10 to 20% EtOAc in PE). Fractions were evaporated to dryness to afford crude 6-(3-chlorobenzyl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-{[2-(trimethyl­silyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4f); yield: 3.20 g (73%) as a yellow oil. Material used crude and not fully isolated.

MS (ES+): m/z = 515 [M + H]⁺.

PdCl₂(dtbpf) (25.3 mg, 0.04 mmol) was added to a solution of K₂CO₃ (107 mg, 0.78 mmol), 4-(6-chloropyrazin-2-yl)morpholine (1c; 93 mg, 0.47 mmol), and crude 4f (200 mg, 0.39 mmol) in 1,4-dioxane (15 mL) and H₂O (3.00 mL). The resulting suspension was stirred at 30 °C for 2 h under N₂. The reaction mixture was quenched with H₂O (150 mL) and extracted with EtOAc (3 × 50 mL). The combined organic layers­ were dried (Na₂SO₄), filtered and evaporated to afford crude 6-(3-chlorobenzyl)-3-(6-morpholinopyrazin-2-yl)-1-{[(2-(trimethylsilyl)ethoxy]methyl}-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4g); yield: 120 mg (56%) as a colourless oil. Material used crude and not fully isolated.

MS (ES+): m/z = 552 [M + H]⁺.

TFA (16.7 μL, 0.22 mmol) was added to 4g (120 mg, 0.22 mmol) in DCM (5 mL). The resulting solution was stirred at RT for 1 h and the solvent was removed under reduced pressure. Residue was redissolved in DMF (5 mL) before ethylenediamine (10.64 mg, 0.18 mmol) was added and the resulting solution stirred at RT for 1 h. The crude product was purified by preparative HPLC. Column: XBridge Prep OBD C18 Column 30 × 150 mm 5 μm; Mobile Phase A: H₂O (10 mmol/L NH₄HCO₃ + 0.1% NH₄OH), Mobile Phase B: MeCN; Flow rate: 60 mL/min; Gradient: 27% B to 55% B in 7 min; 254/220 nm). Fractions containing the desired compound were evaporated to dryness to afford 6-(3-chlorobenzyl)-3-(6-morpholinopyrazin-2-yl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one (4); yield: 49.3 mg (66%); white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.55–3.59 (m, 4 H), 3.73–3.78 (m, 4 H), 5.22 (s, 2 H), 7.22 (d, J = 7.2 Hz, 1 H), 7.25–7.28 (m, 1 H), 7.32–7.39 (m, 4 H), 8.07 (s, 1 H), 8.09 (s, 1 H), 8.40 (s, 1 H), 12.47 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.60, 49.39, 65.82, 102.03, 114.90, 124.72, 126.24, 126.92, 127.23, 127.30, 127.39, 127.90, 129.57, 129.83, 130.46, 133.07, 140.71, 146.79, 154.10, 154.20.

MS (ES+): m/z = 422 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₂H₂₀ClN₅O₂: 422.1378; found: 422.13776.

Synthesis of 3-Benzyl-7-(6-morpholinopyrazin-2-yl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one (5)

Ethyl 3-Amino-4-bromo-1H-pyrrole-2-carboxylate (5b) [27]

Ethyl 3-amino-1H-pyrrole-2-carboxylate hydrochloride (5a;[28] 2.00 g, 10.49 mmol) was dissolved in H₂O (50 mL) and loaded onto an SCX cartridge. The column was washed with MeOH (3 column volumes), then the product was eluted with 1 M NH₃/MeOH solution. The basic fraction containing the desired product was concentrated under reduced pressure to give ethyl 3-amino-1H-pyrrole-2-carboxylate (1.617 g, assumed quantitative) as a brown gum, which was used crude and not isolated.

NBS (5.88 g, 33.03 mmol) was added portionwise over 30 min to an ice bath cooled solution of crude ethyl 3-amino-1H-pyrrole-2-carboxylate (5.092 g, 33.03 mmol) in CHCl₃ (15 mL) and AcOH (15 mL). The reaction mixture was allowed to warm to RT and stirred for a further 90 min. H₂O (100 mL) was added and the mixture extracted with DCM (2 × 100 mL). The combined organics were passed through a phase separating cartridge and concentrated in vacuo to give a dark orange gum. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 25% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 2.55 g (33%); off-white solid (Lit.[27] mp 92 °C).

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.27 (t, J = 7.1 Hz, 4 H), 4.21 (q, J = 7.1 Hz, 2 H), 4.84 (s, 2 H), 6.90 (d, J = 3.6 Hz, 1 H), 11.14 (s, 1 H).

MS (ES+): m/z = 233 [M + H]⁺.

7-Bromo-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one (5c)[29]

Formamidine acetate (0.648 g, 6.22 mmol) was added to a solution of ethyl 3-amino-4-bromo-1H-pyrrole-2-carboxylate (5b; 0.967 g, 4.15 mmol) in EtOH (15 mL) and the reaction mixture stirred at 105 °C for 16 h and cooled to RT. The resulting precipitate was collected by filtration, washed with EtOH and dried; yield: 0.818 g (92%); beige solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 7.57 (s, 1 H), 7.86 (s, 1 H), 12.06 (s, 1 H), 12.50 (s, 1 H).

MS (ES+): m/z = 216 [M + H]⁺.

tert-Butyl 7-Bromo-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5d)

Di-tert-butyl dicarbonate (0.826 g, 3.78 mmol) was added to a stirred solution of 7-bromo-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one (5c; 0.81 g, 3.78 mmol) and DMAP (0.092 g, 0.76 mmol) in DMF (30 mL) at RT. The reaction mixture was stirred for 16 h. The solvents were then removed in vacuo to give a brown solid. This was then triturated with Et₂O, filtered and dried to give a beige solid (0.848 g, 71%), which consisted of mainly Boc-deprotected material, presumably arising from thermal deprotection that occurred due to the high temperatures that were needed to remove the DMF in vacuo. The mixture was redissolved in DMF (30 mL) before di-tert-butyl dicarbonate (0.780 g, 3.57 mmol) and DMAP (0.087 g, 0.71 mmol) were added at RT. The reaction mixture was stirred for 16 h. The mixture was diluted with DCM (50 mL), washed with H₂O (100 mL), organic layer passed through a phase separating cartridge and concentrated in vacuo. The crude product was purified by flash silica chromatography (eluent: gradient 0 to 100% EtOAc in heptane followed by 10% MeOH in EtOAc) and pure fractions were evaporated to dryness; yield: 0.425 g (38%); white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.58 (s, 9 H), 8.04 (s, 1 H), 8.07 (s, 1 H), 12.41 (s, 1 H).

MS (ES–): m/z = 312 [M – H]^–.

tert-Butyl 3-Benzyl-7-bromo-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5e)

NaH (60% in mineral oil; 58.8 mg, 1.47 mmol) was added portionwise to tert-butyl 7-bromo-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5d; 420 mg, 1.34 mmol) in DMF (10 mL) at <5 °C under N₂. The resulting mixture was allowed to warm to RT and stirred for 30 min. To this was added benzyl bromide (0.175 mL, 1.47 mmol) dropwise over a period of 2 min and the mixture stirred for 2 h. The mixture was quenched with sat. aq NH₄Cl (3 mL), partitioned between DCM (50 mL) and H₂O (50 mL) and the organic layer collected. The aqueous layer was further extracted with DCM (50 mL). The combined organic layers were washed with brine and passed through a phase separating cartridge and evaporated to dryness to afford crude product. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 50% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 408 mg (75%); white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.55 (s, 9 H), 5.21 (s, 2 H), 7.15–7.43 (m, 5 H), 8.09 (s, 1 H), 8.60 (s, 1 H).

MS (ES+): m/z = 244 [M + H]⁺.

4-(6-Bromopyrazin-2-yl)morpholine (5g)[30]

Morpholine (1b; 0.811 mL, 9.27 mmol) was added to 2,6-dibromopyrazine (5f; 2.004 g, 8.42 mmol) and Et₃N (1.409 mL, 10.11 mmol) in MeCN (200 mL) at 0 °C. The reaction mixture was then allowed to warm to RT and stirred for 30 min before heating to 80 °C for 2 h. The solvents were removed in vacuo and the residue dissolved in DCM (200 mL) and washed with sat. aq NH₄Cl (200 mL). The organic layer was passed through a phase separating cartridge and concentrated in vacuo; yield: 1.938 g (94%); yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.45–3.58 (m, 4 H), 3.64–3.75 (m, 4 H), 7.95 (s, 1 H), 8.23–8.36 (m, 1 H).

MS (ES+): m/z = 244 [M + H]⁺.

4-[6-(Trimethylstannyl)pyrazin-2-yl]morpholine (5h)

PdCl₂(PPh₃)₂ (0.040 g, 0.06 mmol) was added to a degassed mixture of 4-(6-bromopyrazin-2-yl)morpholine (5g; 0.281 g, 1.15 mmol) and 1,1,1,2,2,2-hexamethyldistannane (0.286 mL, 1.38 mmol) in 1,4-dioxane (5 mL). The reaction mixture was stirred at 60 °C for 1 h. The mixture was then cooled to RT and stirred overnight before being diluted with EtOAc (100 mL) and washed with H₂O (100 mL). The layers were separated and the aqueous phase was extracted further with EtOAc (2 × 50 mL). The combined organic layers were dried (MgSO₄), filtered and the solvent removed in vacuo to give crude material. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 50% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 0.162 g (43%); colourless gum.

¹H NMR (500 MHz, DMSO-d ₆): δ = 0.29 (s, 9 H), 3.37–3.62 (m, 4 H), 3.63–3.79 (m, 4 H), 7.91 (s, 1 H), 8.12 (s, 1 H).

MS (ES+): m/z = 330 [M + H]⁺.

tert-Butyl 3-Benzyl-7-(6-morpholinopyrazin-2-yl)-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5i)

PdCl₂(dtbpf) (16.69 mg, 0.03 mmol) was added to a degassed mixture of 4-[6-(trimethylstannyl)pyrazin-2-yl]morpholine (5h; 84 mg, 0.26 mmol) and tert-butyl 3-benzyl-7-bromo-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5e; 104 mg, 0.26 mmol) in DMF (1.5 mL) under N₂. The resulting solution was stirred at 80 °C for 1 h. An additional amount of 5h (84 mg, 0.26 mmol) was added and stirred at 80 °C for a further 2 h. The reaction mixture was cooled to RT, diluted with EtOAc (50 mL), washed with H₂O (100 mL), and the organic layer was passed through a phase separating cartridge and concentrated in vacuo. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 25.0 mg (20%); beige solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 1.58 (s, 9 H), 3.5–3.67 (m, 4 H), 3.67–3.83 (m, 4 H), 5.23 (d, J = 22.5 Hz, 2 H), 7.13–7.46 (m, 5 H), 8.25 (s, 1 H), 8.31 (s, 1 H), 8.67 (s, 1 H), 8.95 (s, 1 H).

MS (ES+): m/z = 489 [M + H]⁺.

3-Benzyl-7-(6-morpholinopyrazin-2-yl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one (5)

TFA (0.25 mL) was added to a stirred solution of tert-butyl 3-benzyl-7-(6-morpholinopyrazin-2-yl)-4-oxo-3H-pyrrolo[3,2-d]pyrimidine-5(4H)-carboxylate (5i; 23 mg, 0.05 mmol) in DCM (0.5 mL). The reaction mixture was stirred for 2 h at RT. The crude product was purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded, column eluted with MeOH before the desired product was eluted using 7 M NH₃/MeOH. The basic fraction was evaporated to dryness; yield: 12.00 mg (66%); white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.58 (t, J = 4.8 Hz, 4 H), 3.73 (t, J = 4.8 Hz, 4 H), 5.26 (s, 2 H), 7.24–7.32 (m, 3 H), 7.35 (d, J = 4.3 Hz, 2 H), 8.02 (d, J = 2.5 Hz, 1 H), 8.11 (s, 1 H), 8.46 (s, 1 H), 8.92 (s, 1 H), 12.64 (s, 1 H, NH).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.26, 47.87, 65.85, 114.66, 118.61, 127.49, 127.96, 128.02, 128.55, 130.14, 137.39, 141.01, 144.74, 145.51, 153.05, 153.84.

MS (ES+): m/z = 389 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₁H₂₀N₆O₂: 389.1721; found: 389.17264.

Synthesis of 5-Benzyl-1-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[3,2-c]pyridin-4(5H)-one (6)

4-[6-(4-Chloro-1H-pyrrolo[3,2-c]pyridin-1-yl)pyrazin-2-yl]morpholine­ (6b)

NaH (60% in mineral oil; 0.205 g, 5.12 mmol) was added to a stirred solution of 4-chloro-1H-pyrrolo[3,2-c]pyridine (6a; 0.710 g, 4.65 mmol) in DMF (20 mL) at RT and the mixture stirred for 15 min. 4-(6-Chloropyrazin-2-yl)morpholine (1c; 1.022 g, 5.12 mmol) was then added and the reaction mixture heated to 120 °C for 4 h. The mixture was cooled to RT. H₂O (100 mL) was added and the resulting precipitate was collected by filtration, washed with H₂O, and dried under high vacuum; yield: 1.086 g (74%); off-white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.59–3.69 (m, 4 H), 3.72–3.82 (m, 4 H), 6.89 (d, J = 3.4 Hz, 1 H), 8.17 (s, 2 H), 8.26 (d, J = 3.6 Hz, 1 H), 8.32 (s, 1 H), 8.37 (s, 1 H).

MS (ES+): m/z = 316 [M + H]⁺.

1-(6-Morpholinopyrazin-2-yl)-1H-pyrrolo[3,2-c]pyridin-4(5H)-one (6c)

NaOAc (29.1 mg, 0.35 mmol) was added to a stirred suspension of 4-[6-(4-chloro-1H-pyrrolo[3,2-c]pyridin-1-yl)pyrazin-2-yl]morpholine (6b; 56 mg, 0.18 mmol) and AcOH (1 mL) and the reaction mixture heated to 130 °C for 24 h. The mixture was cooled to RT. The crude product was purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded, column eluted with MeOH before the desired product was eluted with 7 M NH₃/MeOH. The basic fraction was evaporated to dryness; yield: 52.0 mg (99%); brown solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.51–3.69 (m, 4 H), 3.69–3.85 (m, 4 H), 6.75 (dd, J = 0.7, 3.4 Hz, 1 H), 7.07 (dd, J = 0.7, 7.3 Hz, 1 H), 7.14 (d, J = 7.3 Hz, 1 H), 7.73 (d, J = 3.4 Hz, 1 H), 8.24 (s, 1 H), 8.28–8.36 (m, 1 H). One exchangeable H not seen.

MS (ES+): m/z = 388 [M + H]⁺.

5-Benzyl-1-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[3,2-c]pyridin-4(5H)-one (6)

To a stirred suspension of 1-(6-morpholinopyrazin-2-yl)-1H-pyrrolo[3,2-c]pyridin-4(5H)-one (6c; 50.0 mg, 0.17 mmol) in DMF (1 mL) at 0 °C was added NaH (60% in mineral oil; 7.40 mg, 0.18 mmol). The mixture was then stirred at 20 °C for 30 min. Benzyl bromide (22 μL, 0.18 mmol) was then added and the mixture stirred at 20 °C for 2 h. The crude product was partially purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded, column eluted with MeOH before the desired product was eluted using 7 M NH₃/MeOH. The basic fraction was evaporated to dryness to afford crude product. The crude product was purified by preparative HPLC (Waters XBridge Prep C18 OBD column, 5 μ silica gel, 30 mm diameter, 100 mm length), using decreasingly polar mixtures of H₂O (containing 1% NH₃) and MeCN as eluents. Fractions containing the desired compound were evaporated to dryness; yield: 21 mg (32%); beige solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.55–3.65 (m, 4 H), 3.70–3.81 (m, 4 H), 5.20 (s, 2 H), 6.80 (dd, J = 0.7, 3.4 Hz, 1 H), 7.15 (dd, J = 0.7, 7.5 Hz, 1 H), 7.2–7.41 (m, 5 H), 7.53 (d, J = 7.5 Hz, 1 H), 7.77 (d, J = 3.4 Hz, 1 H), 8.26 (s, 1 H), 8.30 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.40, 50.05, 65.65, 96.60, 107.01, 117.48, 123.17, 123.78, 127.30, 127.55, 128.32, 128.48, 133.04, 137.34, 138.15, 145.05, 153.21, 158.23.

MS (ES+): m/z = 388 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₂H₂₁N₅O₂: 388.1768; found: 388.17798.

Synthesis of 2-Benzyl-6-(6-morpholinopyrazin-2-yl)pyrrolo[1,2-a]pyrazin-1(2H)-one (7)

5-Bromo-1H-pyrrole-2-carboxylic Acid (7b) [31]

1H-Pyrrole-2-carboxylic acid (7a; 3.9 g, 35.10 mmol) was dissolved in THF (40 mL) at RT under N₂ and the resultant solution was cooled to 0 °C. NBS (6.12 g, 34.4 mmol) was added in 2 portions (3.0 g followed by 3.12 g). The reaction was quenched with sat. aq NH₄Cl, diluted with EtOAc, and the layers separated. The aqueous layer was extracted with EtOAc (2 ×), organics combined, dried (MgSO₄), filtered and solvent removed in vacuo to give crude material as a green solid. DCM was added, leaving a suspension, which was filtered off under vacuum to give a grey solid (Solid A). The filtrate was concentrated to dryness under vacuum, to give a dark brown solid (Solid B). Solid A was dissolved in EtOAc, partitioned with sat. aq NaHCO₃ (2 ×) to remove residiual succinamide. The aqueous layer was acidified to pH 1 using aq 2 M HCl, which caused a solid to crash out of solution; this was collected by filtration under vacuum and dried to give the undesired regioisomer 4-bromo-1H-pyrrole-2-carboxylic acid (3.11 g, 47%) as an off-white solid. Solid B was dissolved in EtOAc, partitioned with sat. aq NaHCO₃ (2 ×) to remove residual succinimide. The aqueous layer was acidified to pH 1 using aq 2 M HCl, extracted with EtOAc (2 ×), and the combined extracts were concentrated in vacuo to give a crude brown solid (2.45 g). The crude solid was purified by reverse phase preparative HPLC (C18 RediSepRf GOLD HP column, 415 g), using decreasingly polar mixtures of H₂O (containing 0.1% formic acid) and MeCN as eluents. Pure fractions containing the desired regioisomer were evaporated to dryness; yield: 1.500 g (22%); beige crystalline solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 6.18 (d, J = 3.8 Hz, 1 H), 6.69 (d, J = 3.8 Hz, 1 H), 12.36 (s, 1 H).

MS (ES+): m/z = 188, 190 [M + H]⁺.

6-Bromopyrrolo[1,2-a]pyrazin-1(2H)-one (7e)[32]

N ¹-[(Ethylimino)methylene]-N ³,N ³-dimethylpropane-1,3-diamine hydrochloride (EDC·HCl; 454 mg, 2.37 mmol) and 1H-benzo[d][1,2,3]triazol-1-ol (HOBt) hydrate (363 mg, 2.37 mmol) were added to a solution of 5-bromo-1H-pyrrole-2-carboxylic acid (7b; 300 mg, 1.58 mmol), (1,3-dioxolan-2-yl)methanamine (0.23 mL, 2.37 mmol), and Et₃N (1.10 mL, 7.89 mmol) in DMF (6 mL) at RT under N₂ and the reaction mixture stirred at RT for 3 h. The mixture was warmed to 35 °C to fully dissolve reactants. After 10 min heating, the reaction mixture was cooled to RT, diluted with DCM and H₂O, and the layers separated. The aqueous phase was extracted with DCM (2 ×), the combined organics washed with brine, dried (MgSO₄), filtered and solvent removed in vacuo to give crude N-[(1,3-dioxolan-2-yl)methyl]-5-bromo-1H-pyrrole-2-carboxamide (7c); yield: 434 mg (1.578 mmol, ∼100%, 50% pure) as an orange liquid. The material was used crude and not fully isolated.

MS (ES+): m/z = 275 [M + H]⁺.

Compound 7c (434 mg, 0.79 mmol) was dissolved in a mixture of acetone (50 mL) and H₂O (4.00 mL) before TsOH·H₂O (1200 mg, 6.31 mmol) was added and the resultant solution heated at reflux overnight. The reaction was allowed to cool, solvent removed in vacuo, redissolved in EtOAc, aand washed with sat. aq NaHCO₃. The organic phase was dried (MgSO₄), filtered and solvent removed in vacuo to give crude 6-bromo-4-hydroxy-3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one (7d); yield: 356 mg (195%, 34% pure ∼66%) as a brown solid. Material used crude and not fully isolated.

MS (ES+): m/z = 231 [M + H]⁺.

Crude 7d (356 mg, 0.52 mmol, 34% pure) was dissolved in MeSO₃H (4 mL, 0.52 mmol) at RT under N₂ before the resulting solution was heated to 45 °C for 2 h. The reaction mixture was allowed to cool, diluted with H₂O (40 mL) and DCM (40 mL), and the layers separated. The aqueous phase was extracted with DCM (2 ×), organics combined, dried (MgSO₄), filtered and solvent removed in vacuo to give a dark brown solid. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane). Fractions containing product were evaporated to dryness to afford 6-bromo­pyrrolo[1,2-a]pyrazin-1(2H)-one (7e); yield: 47.0 mg (42%); brown fluffy solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 6.71 (d, J = 4.2 Hz, 1 H), 6.73 (d, J = 5.9 Hz, 1 H), 6.97 (dd, J = 0.8, 4.2 Hz, 1 H), 7.14 (dd, J = 0.8, 5.8 Hz, 1 H), 10.67 (s, 1 H).

MS (ES+): m/z = 213 [M + H]⁺.

2-Benzyl-6-bromopyrrolo[1,2-a]pyrazin-1(2H)-one (7f)

NaH (60% in mineral oil; 6.22 mg, 0.26 mmol) was added to 6-bromopyrrolo[1,2-a]pyrazin-1(2H)-one (7e; 46 mg, 0.22 mmol) in DMF (2 mL) at 0 °C under N₂. The resulting mixture was allowed to warm to RT and stirred for 30 min. To this was added benzyl bromide (26 μL, 0.22 mmol) at RT and then allowed to stir for 1 h. The reaction was quenched with sat. aq NH₄Cl (1 mL), partitioned between DCM (20 mL) and H₂O (20 mL), the layers separated, and the aqueous layer was extracted with DCM (25 mL). The combined organic layers were washed with brine, dried (MgSO₄), filtered and the solvent was removed in vacuo to give crude material. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 30% EtOAc­ in heptane) and pure fractions were evaporated to dryness; yield: 45.0 mg (69%); white solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 5.05 (s, 2 H), 6.75 (d, J = 4.2 Hz, 1 H), 7.01 (dd, J = 0.8, 4.2 Hz, 1 H), 7.05 (d, J = 6.0 Hz, 1 H), 7.25–7.36 (m, 6 H).

MS (ES+): m/z = 388 [M + H]⁺.

2-Benzyl-6-(6-morpholinopyrazin-2-yl)pyrrolo[1,2-a]pyrazin-1(2H)-one (7)

PdCl₂(dtbpf) (9.67 mg, 0.01 mmol) was added to a degassed mixture of 4-[6-(trimethylstannyl)pyrazin-2-yl]morpholine (5h; 105 mg, 0.30 mmol) and 2-benzyl-6-bromopyrrolo[1,2-a]pyrazin-1(2H)-one (7f; 45 mg, 0.15 mmol) in DMF (1.5 mL) under N₂. The resulting solution was stirred at 80 °C for 30 min. An additional amount of 5h (71 mg, 0.20 mmol) was added and heating continued at 80 °C for a further 30 min. The reaction mixture was cooled to RT, diluted with EtOAc (25 mL), washed with H₂O (50 mL), and the layers separated. The aqueous layer was extracted with EtOAc (2 × 25 mL), combined organics washed with H₂O, dried (MgSO₄), filtered and solvent removed in vacuo to give crude material as a brown solid. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 60% EtOAc in heptane). Fractions containing product were evaporated to dryness, but product had completely co-eluted with homocoupled material, to give a yellow solid (32 mg). Product purified further by preparative HPLC (Waters XBridge Prep C18 OBD column, 5 μ silica gel, 30 mm diameter, 100 mm length), using decreasingly polar mixtures of H₂O (containing 1% NH₃) and MeCN as eluents. Fractions containing the desired compound were evaporated to dryness; yield: 8.50 mg (15%); beige solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.53–3.58 (m, 4 H), 3.71–3.77 (m, 4 H), 5.06 (s, 2 H), 7.00 (d, J = 6.2 Hz, 1 H), 7.06 (dd, J = 0.6, 4.3 Hz, 1 H), 7.26–7.31 (m, 2 H), 7.31–7.37 (m, 4 H), 8.23 (d, J = 0.5 Hz, 1 H), 8.41 (dd, J = 0.6, 6.2 Hz, 1 H), 8.42 (d, J = 0.4 Hz, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.53, 48.88, 65.72, 107.74, 110.42, 114.03, 118.84, 126.24, 126.44, 127.51, 127.70, 128.60, 128.73, 130.94, 137.43, 143.00, 153.45, 154.88.

MS (ES+): m/z = 388 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₂H₂₁N₅O₂: 388.1768; found: 388.17837.

Synthesis of 7-Benzyl-3-(6-morpholinopyrazin-2-yl)imidazo[1,5-a]pyrazin-8(7H)-one (8)

N-[(3-Chloropyrazin-2-yl)methyl]-6-morpholinopyrazine-2-carboxamide (8c)

HATU (601 mg, 1.58 mmol) was added in one portion to 6-morpholinopyrazine-2-carboxylic acid (8a;[33] 301 mg, 1.44 mmol), (3-chloropyrazin-2-yl)methanamine dihydrochloride (8b;[34] (311 mg, 1.44 mmol), and DIPEA (1.251 mL, 7.18 mmol) in DMF (11.69 mL) at 25 °C under N₂. The resulting mixture was stirred at 25 °C for 18 h. The reaction was quenched by the addition of H₂O (40 mL) and the resulting precipitate was collected by filtration and washed well with H₂O, and dried; yield: 480 mg (∼100%); pale green solid. The product was used in the next step without further purification.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.67 (dt, J = 3.3, 6.1 Hz, 4 H), 3.73 (dd, J = 3.6, 5.6 Hz, 4 H), 4.73 (d, J = 5.8 Hz, 2 H), 8.38 (d, J = 0.4 Hz, 1 H), 8.42–8.44 (m, 1 H), 8.51 (d, J = 0.5 Hz, 1 H), 8.61 (d, J = 2.5 Hz, 1 H), 9.17 (t, J = 5.9 Hz, 1 H).

MS (ES+): m/z = 335 [M + H]⁺.

4-[6-(8-Chloroimidazo[1,5-a]pyrazin-3-yl)pyrazin-2-yl]morpholine (8d)

DMF (1 drop) was added to N-[(3-chloropyrazin-2-yl)methyl]-6-morpholinopyrazine-2-carboxamide (8c; 404 mg, 1.21 mmol) in POCl₃ (6034 μL) at 25 °C. The resulting mixture was stirred at reflux (106 °C) for 4 h. The mixture was allowed to cool to RT, evaporated to dryness, dissolved in EtOAc and washed sequentially with sat. aq NaHCO₃, H₂O, and brine. The organic layer was then dried (MgSO₄), filtered, and silica gel added to preabsorb crude product and evaporated to dryness. The crude product was purified by flash silica gel (40 g, Grace chemicals) chromatography, solid load (eluent: gradient 10 to 100% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 170 mg (45%); yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.61–3.67 (m, 4 H), 3.76–3.82 (m, 4 H), 7.63 (d, J = 5.0 Hz, 1 H), 8.11 (d, J = 0.9 Hz, 1 H), 8.41 (s, 1 H), 8.72 (s, 1 H), 9.26 (dd, J = 0.9, 5.0 Hz, 1 H).

MS (ES+): m/z = 317 [M + H]⁺.

3-(6-Morpholinopyrazin-2-yl)imidazo[1,5-a]pyrazin-8(7H)-one (8e)

Aq 5 M HCl (6.0 mL, 30.06 mmol) was added to 4-[6-(8-chloroimidazo[1,5-a]pyrazin-3-yl)pyrazin-2-yl]morpholine (8d; 170 mg, 0.54 mmol) at 25 °C. The resulting mixture was stirred at 80 °C for 2.5 h. The reaction mixture was allowed to cool to RT, diluted with H₂O, and then the crude product was purified by ion exchange chromatography, using a SCX-2 column (20 g). The column was washed with MeOH before the reaction mixture was loaded, column eluted with MeOH before the desired product was eluted using 1 M NH₃/MeOH (200 mL), followed by a mixture of DCM/1 N NH₃ in MeOH (100 mL), then finally 1 N NH₃ in MeOH (200 mL) again. The combined basic fractions were evaporated to dryness; yield: 72.0 mg (45%); yellow solid.

Yield low due to product precipitating on SCX column after 1 N NH₃ in MeOH was added.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.57–3.63 (m, 4 H), 3.74–3.8 (m, 4 H), 6.81 (t, J = 5.7 Hz, 1 H), 7.93 (d, J = 0.7 Hz, 1 H), 8.34 (d, J = 6.0 Hz, 1 H), 8.38 (d, J = 0.5 Hz, 1 H), 8.65 (d, J = 0.4 Hz, 1 H), 10.88 (d, J = 5.4 Hz, 1 H).

MS (ES+): m/z = 299 [M + H]⁺.

7-Benzyl-3-(6-morpholinopyrazin-2-yl)imidazo[1,5-a]pyrazin-8(7H)-one (8)

NaH (60% in mineral oil; 9.59 mg, 0.24 mmol) was added in one portion to 3-(6-morpholinopyrazin-2-yl)imidazo[1,5-a]pyrazin-8(7H)-one (8e; 65.0 mg, 0.22 mmol) in DMF (2.15 mL) at RT under N₂. The resulting mixture was allowed to stir for 15 min. To this solution was added benzyl bromide (28.5 μL, 0.24 mmol) dropwise over a period of 30 seconds at RT and then allowed to stir for 18 h. The reaction was quenched with sat. aq NH₄Cl (1 mL) before being diluted with H₂O (20 mL) and stirred for 15 min. The precipitate was collected by filtration, washed sequentially with H₂O, heptane, and finally Et₂O and then dried under vacuum at 50 °C; yield: 55.0 mg (65%); yellow solid.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.55–3.61 (m, 4 H), 3.72–3.79 (m, 4 H), 5.07 (s, 2 H), 7.09 (d, J = 6.2 Hz, 1 H), 7.30 (dt, J = 4.6, 9.4 Hz, 1 H), 7.35 (d, J = 4.7 Hz, 4 H), 7.98 (s, 1 H), 8.36–8.42 (m, 2 H), 8.65 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 44.51, 48.76, 65.67, 106.43, 121.21, 125.09, 127.63, 127.73, 128.64, 130.49, 130.88, 131.18, 136.99, 138.31, 141.24, 153.41, 154.48.

MS (ES+): m/z = 389 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₁H₂₀N₆O₂: 389.1721; found: 389.1721.

Synthesis of 5-(3,4-Dichlorobenzyl)-2-(6-morpholinopyrazin-2-yl)-4,5-dihydropyrrolo[3,4-b]pyrrol-6(1H)-one (9)

tert-Butyl 5-(3,4-Dichlorobenzyl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9b)

NaH (60% in mineral oil; 26.5 mg, 0.66 mmol) was added to tert-butyl 6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9a;[21] 134 mg, 0.60 mmol) in DMF (4 mL) under N₂. The resulting solution was stirred at 20 °C for 30 min. 4-(Bromomethyl)-1,2-dichlorobenzene (145 mg, 0.60 mmol) in DMF (1 mL) was then added to the reaction and stirring was continued overnight. The reaction mixture was quenched with sat. aq NH₄Cl (25 mL), extracted with EtOAc (25 mL), the organic layer was dried (MgSO₄), filtered and evaporated to afford a crude product. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 25% EtOAc in heptane) and pure fractions were evaporated to dryness; yield: 170 mg (74%); white solid.

¹H NMR (500 MHz, CDCl₃): δ = 1.57 (s, 9 H), 4.53 (s, 2 H), 5.25 (s, 2 H), 6.12 (d, J = 2.5 Hz, 1 H), 6.93 (d, J = 2.5 Hz, 1 H), 7.16 (dd, J = 2.1, 8.3 Hz, 1 H), 7.32 (d, J = 1.9 Hz, 1 H), 7.39 (d, J = 8.2 Hz, 1 H).

MS (ES+): m/z = 323 [M + H]⁺.

tert-Butyl 5-(3,4-Dichlorobenzyl)-2-(6-morpholinopyrazin-2-yl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9d)

(1,5-Cyclooctadiene)(methoxy)iridium(I) dimer (4.73 mg, 7.13 μmol) was added in one portion to a degassed solution of tert-butyl 5-(3,4-dichlorobenzyl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9b; 170 mg, 0.45 mmol), bis(pinacolato)diboron (119 mg, 0.47 mmol), and 4,4′-di-tert-butyl-2,2′-dipyridyl (BBBPY; 3.83 mg, 0.01 mmol) in MTBE (4 mL) under N₂. The resulting solution was stirred at 60 °C for 2 h. The reaction mixture was then evaporated to dryness to give a solid. The solid was dissolved in DCM and passed through a silica gel plug, eluting with DCM. The filtrate was concentrated to give crude tert-butyl 5-(3,4-dichlorobenzyl)-6-oxo-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9c) (240 mg, 106%) as a pink gum. The product was found to be a mixture of regisomers, undesired tert-butyl 5-(3,4-dichlorobenzyl)-6-oxo-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate and desired 9c (ratio 1:2 respectively). Material used crude and not fully isolated.

MS (ES+): m/z = 507 [M + H]⁺.

Pd(PPh₃)₄ (54.7 mg, 0.05 mmol) was added in one portion to a degassed solution of 4-(6-chloropyrazin-2-yl)morpholine (1c; 94 mg, 0.47 mmol), crude tert-butyl 5-(3,4-dichlorobenzyl)-6-oxo-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9c; 240 mg, 0.47 mmol) (mixture of regioisomers, 1:2, see previous step), and Na₂CO₃ (0.473 mL, 0.95 mmol) in DME (4 mL) under N₂. The resulting solution was stirred at 85 °C for 1 h. The reaction mixture was diluted with DCM (50 mL) and washed with H₂O (50 mL). The organic layer was dried (MgSO₄), filtered and evaporated to afford crude product. The crude product was purified by flash silica gel chromatography (eluent: gradient 0 to 100% EtOAc in heptane). Pure fractions were evaporated to dryness to afford undesired tert-butyl 5-(3,4-dichlorobenzyl)-3-(6-morpholinopyrazin-2-yl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (44.0 mg, 17%) (second eluting) as a yellow solid and desired regioisomer tert-butyl 5-(3,4-dichlorobenzyl)-2-(6-morpholinopyrazin-2-yl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9d) (34.0 mg, 13%) (first eluting) as a yellow solid.

¹H NMR (500 MHz, CDCl₃): δ = 1.57 (s, 9 H), 3.29–3.40 (m, 4 H), 3.67–3.77 (m, 4 H), 4.60 (s, 2 H), 5.82 (s, 2 H), 6.61 (s, 1 H), 6.90 (dd, J = 2.1, 8.3 Hz, 1 H), 7.13 (d, J = 2.0 Hz, 1 H), 7.30 (d, J = 8.2 Hz, 1 H), 8.01 (s, 1 H), 8.19 (s, 1 H).

MS (ES+): m/z = 488 [M + H]⁺.

5-(3,4-Dichlorobenzyl)-2-(6-morpholinopyrazin-2-yl)-4,5-dihydropyrrolo[3,4-b]pyrrol-6(1H)-one (9)

TFA (0.048 mL, 0.62 mmol) was added to tert-butyl 5-(3,4-dichlorobenzyl)-2-(6-morpholinopyrazin-2-yl)-6-oxo-5,6-dihydropyrrolo[3,4-b]pyrrole-1(4H)-carboxylate (9d; 34 mg, 0.06 mmol) in DCM (2 mL). The resulting solution was stirred at 20 °C for 1 h. The crude product was purified by ion exchange chromatography, using an SCX column. The column was washed with MeOH before the reaction mixture was loaded, column eluted with MeOH before the desired product was eluted using 1 M NH₃/MeOH. The basic fraction was evaporated to dryness; yield: 16.90 mg (61%); colourless gum.

¹H NMR (500 MHz, DMSO-d ₆): δ = 3.28 (t, J = 4.9 Hz, 4 H), 3.58 (t, J = 4.9 Hz, 4 H), 4.18 (s, 2 H), 5.82 (s, 2 H), 6.86 (dd, J = 8.4, 2.1 Hz, 1 H), 6.90 (s, 1 H), 7.24 (d, J = 2.0 Hz, 1 H), 7.53 (d, J = 8.7 Hz, overlapped, 1 H), 8.10 (s, 1 H, NH), 8.14 (s, 1 H), 8.30 (s, 1 H).

¹³C NMR (126 MHz, DMSO-d ₆): δ = 40.80, 44.23, 47.41, 65.59, 105.60, 126.02, 127.83, 128.63, 129.35, 130.58, 130.89, 130.98, 131.61, 134.75, 135.97, 140.34, 143.44, 153.16, 163.20.

MS (ES+): m/z = 444 [M + H]⁺.

HRMS: m/z [M + H]⁺ calcd for C₂₁H₁₉Cl₂N₅O₂: 444.0994; found: 444.09842.

Conflict of Interest

The authors declare no conflict of interest.

Acknowledgment

We would like to thank all colleagues at AstraZeneca who were involved in the work reported in this manuscript. This includes all project team members and functions including compound purification, compound handling and technical support across the organisation.

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Corresponding Author

Publication History

Received: 01 October 2021

Accepted after revision: 29 November 2021

Article published online:
26 January 2022

© 2022. Thieme. All rights reserved

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

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