Оптимізація та масштабування методу синтезу похідних азаіндолу

In this study, an optimized method for the synthesis of azaindoles was developed and successfully scaled up to a 100 g batch. Improved yields were observed when using electron-deficient azaheterocycles and substrates bearing electron-withdrawing substituents. 6-Chloro-1H-pyrrolo[3,2-c]pyridine was s...

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Опубліковано в:Журнал органічної та фармацевтичної хімії
Дата:2025
Том:23
Випуск:3
Сторінки:4-10
ISSN:2518-1548
Автори та афіліації:
  • Mykyta V. Kordubailo — Institute of Organic Chemistry of the National Academy of Sciences of Ukraine; Enamine Ltd
  • Andrey A. Tolmachev — Taras Shevchenko National University of Kyiv — ORCID: 0009-0001-4351-2829
Автори: Kordubailo, Mykyta V., Tolmachev, Andrey A.
Формат: Стаття
Мова:Англійська
Опубліковано: National University of Pharmacy 2025
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Назва журналу:Journal of Organic and Pharmaceutical Chemistry
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Journal of Organic and Pharmaceutical Chemistry
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author Kordubailo, Mykyta V.
Tolmachev, Andrey A.
author_facet Kordubailo, Mykyta V.
Tolmachev, Andrey A.
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author_sort Kordubailo, Mykyta V.
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container_title Журнал органічної та фармацевтичної хімії
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description In this study, an optimized method for the synthesis of azaindoles was developed and successfully scaled up to a 100 g batch. Improved yields were observed when using electron-deficient azaheterocycles and substrates bearing electron-withdrawing substituents. 6-Chloro-1H-pyrrolo[3,2-c]pyridine was selected for further functionalization using a carbonylation protocol involving carbon monoxide. As a result, novel and promising building blocks for medicinal chemistry were obtained.
doi_str_mv 10.24959/ophcj.25.323307
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fulltext ISSN 2308-8303 (Print) / 2518-1548 (Online) 3 Original Research http://ophcj.nuph.edu.ua UDC (542.06+542.9):547.752 M. V. Kordubailo1,2, A. A. Tolmachev3 1 Institute of Organic Chemistry of the National Academy of Sciences of Ukraine, 5 Akademik Kuhar str., 02094 Kyiv, Ukraine 2 Enamine Ltd, 78 Winston Churchill str., 02094 Kyiv, Ukraine 3 Taras Shevchenko National University of Kyiv, 60 Volodymyrska str., 01033 Kyiv, Ukraine Optimization and Scaling up of the Azaindole Derivatives Synthesis Abstract In this study, an optimized method for the synthesis of azaindoles was developed and successfully scaled up to a 100 g batch. Improved yields were observed when using electron-deficient azaheterocycles and substrates bearing electron-withdrawing substituents. 6-Chloro-1H-pyrrolo[3,2-c]pyridine was selected for further functionalization using a carbonylation protocol involving carbon monoxide. As a result, novel and promising building blocks for medicinal chemistry were obtained. Keywords: azaindoles; Sonogashira coupling; Larock synthesis; carbonylation М. В. Кордубайло1,2, А. О. Толмачов3 1 Інститут органічної хімії Національної академії наук України, вул. Академіка Кухаря, 5, м. Київ, 02094, Україна 2 ТОВ НВП «Єнамін», вул. Вінстона Черчилля, 78, м. Київ, 02094, Україна 3 Київський національний університет імені Тараса Шевченка, вул. Володимирська, 60, м. Київ, 01033, Україна Оптимізація та масштабування методу синтезу похідних азаіндолу Анотація У цьому дослідженні було розроблено оптимізований метод синтезу азаіндолів, який успішно масштабовано для одер- жання до 100 г цільової сполуки. Кращі виходи спостерігали в разі використання електронодефіцитних азагетероциклів та замісників з електронно-акцепторними властивостями. Для подальшої функціоналізації було обрано 6-хлоро-1H- піроло[3,2-c]піридин шляхом його карбонілювання дією карбон(ІІ) оксиду. Внаслідок цього було одержано нові пер- спективні будівельні блоки для потреб медичної хімії. Ключові слова: азаіндоли; реакція Соногашіри; синтез Ларока; карбонілювання Citation: Kordubailo, M. V.; Tolmachev, A. A. Optimization and Scaling up of the Azaindole Derivatives Synthesis. Journal of Organic and Pharmaceutical Chemistry 2025, 23 (3), 3 – 10. https://doi.org/10.24959/ophcj.25.323307 Supporting information: Copies of 1H, 13C, and 19F NMR spectra of the synthesized compounds. Received: 16 June 2025; Revised: 12 September 2025; Accepted: 19 September 2025 Copyright© 2025, M. V. Kordubailo, A. A. Tolmachev. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0). Funding: The author received no specific funding for this work. Conflict of interests: The authors have no conflict of interests to declare. ■ Introduction Azaindoles are compounds composed of fused azaheterocyclic and pyrrole rings, forming aro- matic frameworks that serve as bioisosteres of in- doles and are structurally similar to purine bases. This structural similarity contributes to their broad spectrum of biological activities, making them valuable in pharmaceuticals, industrial ap- plications, and natural product chemistry [1 – 4]. According to the SciFinder® database, azain- doles have increasingly attracted research at- tention since 2000 (Figure 1). Since 2004, due to their recognized antiviral properties and in- fluenced by global health crises, the number of publications on azaindoles has nearly doubled. ISSN 2308-8303 (Print) / 2518-1548 (Online) 4 Журнал органічної та фармацевтичної хімії 2025, 23 (3) Currently, over 100 articles related to azaindoles are published annually [5]. Numerous synthetic approaches have been de- veloped for azaindole formation, predominantly involving the assembly of a pyrrole ring onto existing azaheterocyclic frameworks. However, methods assembling azaheterocycles onto a pyrrole core have also been documented (Figure 2) [5, 6]. ■ Results and discussions Taking into account the significant range of biological activities exhibited by azaindoles dis- covered over the past two decades, optimizing synthetic routes remains critically important. This study aimed to validate and optimize syn- thetic methods across various electron-deficient azaheterocycles, such as pyridine, pyrazine, and pyrimidine. The Larock’s synthetic approach was select- ed to achieve the research purposes due to its versatility and potential for structural diversity. This methodology involves a two-step process: the Sonogashira coupling using TMS-acetylene, followed by the heterocyclization mediated by KOtBu [7 – 11]. Seven azaindole derivatives were chosen for the synthesis, including compounds (3a, 3c, 3g) previously described to establish a more convenient and efficient method. For example, the synthesis of 5H-pyrrolo[2,3-b]pyrazine deriva- tive (3a) via N-mesyl amino pyrazine reported earlier faced difficulties at the initial stage, resulting in low overall yields [12]. Similarly, the synthesis of 6-chloro-1H-pyrrolo[3,2-c]pyri- dine (3c) involved a complicated multi-step cat- alytic oxidation [13]. Additionally, the synthesis of 7-methyl-1H-pyrrolo[3,2-b]pyridine (3g) was previously achieved through the Bartoli method with only 18 % yield [14] or a multistep Suzuki coupling [15]. Derivatives 3b, 3d, 3e, and 3f have not been previously reported. Commercially available amines were utilized for synthesizing 3a, 3c, 3f, and 3g derivatives, namely 3-chloropyrazin-2-amine (1a), 5-bromo- 2-chloropyridin-4-amine (1c), 2-chloro-5-(trifluo- romethyl)pyridin-3-amine (1f), and 2-bromo-4-me- thylpyridin-3-amine (1g). 5-Bromo-2-methylpy- rimidin-4-amine (1b) was obtained with a high yield via the halogen reduction using Pd/C fol- lowed by the bromination (Scheme 1) [16, 17]. 3-Iodo-2-methoxypyridin-4-amine (1d) was pre- pared by the iodination using NIS in acetonitri- le at reflux conditions [18]. For 2-bromo-6-(trifluo- romethyl)pyridin-3-amine (1e), the bromination with NBS was conducted in acetonitrile instead of CHCl3, significantly reducing the formation of regioisomers [19]. The Sonogashira reaction was scaled up to 100 g for each amine, and intermediates 2a – g were purified by flash chromatography, result- ing in excellent yields (Scheme 2). The lowest yield (64.3 %) was noted for alkyne 2c due to side reactions employing chlorine atoms. The optimal cyclization conditions involved the use of 1.2 equiv. Figure 1. The published papers dedicated to azaindoles H N R R X N Me R NH2 Me R R NH2 X R NH2 N H R NN NN N Figure 2. Main strategies toward azaindoles N N NH2 1b Me Cl N N NH2Me N N NH2Me Br H2, Pd/C NaHCO3, MeOH, rt, 16 h AcOH, NaHCO3, rt, 16 h Br2 Scheme 1. The synthesis of starting pyrimidine 1b ISSN 2308-8303 (Print) / 2518-1548 (Online) 5 Journal of Organic and Pharmaceutical Chemistry 2025, 23 (3) of KOtBu in THF. Compounds 2 with electron- withdrawing substituents, such as CF3 (2e, 2f) and chlorine (2c), along with a weakly electron- donating methyl group (2g), secured higher yields of the target azaindoles 3 of about 70 %. At the same time, pyrazine and pyrimidine derivatives (3a, 3b) were obtained with 55 – 57 % yields simi- lar to the methoxy derivative 3d (56.1 %). Derivative 3c, known for its biological activi- ty [20, 21], offered the additional synthetic flex- ibility due to its halogen substituent. The cata- lytic carbonylation with CO in the methanol me- dium provided the corresponding ester 4c with a high yield, which after the acidic hydrolysis yielded carboxylic acid 7c (Scheme 3). At the same time, the reduction of the ester with LiAlH4 yielded alcohol 5c, which was likely to be a va- luable intermediate for MedChem research. The reaction of 5c with SOCl2 produced chloro- methyl derivative 8c, while the oxidation with IBX in EtOAc yielded aldehyde 6c in a moderate 53 % yield. The corresponding amine 10c was also synthesized via azide intermediate 9c, formed using DPPA-DBU conditions, followed by the Staudinger reduction, without the intermediate purification. ■ Conclusion In this study, an optimized method for the azaindole synthesis was reviewed and success- fully scaled up to a 100 g batch size. Higher yields were achieved with electron-deficient azahetero- cycles bearing electron-withdrawing substituents. Additionally, 6-chloro-1H-pyrrolo[3,2-c]pyridine was selected for further functionalization, leading 1a g– N N H N N H N N N H Me N N H F3C N N N H OMe Cl 3a, 55.2 % N N H F3C N N H Me X R NH2 N TEA, dioxane TMS + CuI, Pd(dppf)Cl2 R NH2 N N H R N 3b, 56.8 % 3c, 73.7 % 3d, 56.1 % 3e, 78.2 % 3f, 74.9 % 3g, 67.0 % N N NH2 TMS N N NH2 TMS N NH2 TMS N NH2 TMS Me Cl OMe N NH2 TMS N NH2 TMS N NH2 TMS F3C F3C Me 2a 100.8 g ( )68.2 % 2b 81.2 g ( )74.4 % 2c 69.7 g ( )64.3 % 2d 67.6 g ( )76.7 % 2e 102.3 g ( )77.9 % 2f 91.2 g ( )70.2 % 2g 90.8 g ( )83.2 % Sonogashira coupling products Target azaindoles 64 83 %– (67 102 g)– 55 78 %– (67 102 g)– scale: 17.2 g scale: 18.4 g scale: 45 g scale: 37.7 g scale: 30.5 g scale: 29.2 g scale: 21.7 g 2 –a g 3 –a g Scheme 2. The synthesis of the target azaindoles: scales and yields N N H Cl 3c N N H MeO2C N N H HO N N H O HN N H Cl N N H N3 N N H NH2 4c, 79 % 5c, 70 % 6c, 53 % 8c, 74 % 9c, 42.8 % 10c, 94.3 % HN N H HO2C 7c, 92 % Cl Cl TEA, Pd(dppf)Cl2 CO, MeOH 120 o C;16 h LiAlH4 THF IBX EtOAc conc. HCl 80 o C SOCl2 CHCl3 DPPA, DBU PPh3, H2O THFDCM Scheme 3. The functionalization of product 3c ISSN 2308-8303 (Print) / 2518-1548 (Online) 6 Журнал органічної та фармацевтичної хімії 2025, 23 (3) to the preparation of novel and promising build- ing blocks suitable for applications in medicinal chemistry. ■ Experimental part 1H and 19F NMR spectra were recorded on a Varian Unity Plus 400 instrument (400 and 376 MHz, respectively), 1H and 13C NMR spec- tra were recorded on a Bruker 170 Avance 500 instrument (500 and 126 MHz, respectively), 13C NMR spectra were also recorded on an Agi- lent ProPulse 600 (151 MHz) spectrometer. The NMR chemical shifts were referenced using the solvent signals at 7.26 and 77.1 ppm for 1H and 13C nuclei, respectively, in CDCl3 and 2.48 and 39.5 ppm for 1H and 13C nuclei, respectively, in DMSO-d6; C6F6 was used as the internal stan- dard for 19F NMR spectra. Mass spectra were ob- tained on an Agilent LC/MSD SL 1100 instru- ment (the atmospheric pressure electrospray ioni- zation (ES-API)) or an Agilent 5890 Series II 5972 GCMS instrument (the electron impact (EI) ionization (70eV)). HRMS experiments were per- formed on an Agilent 6224 TOF LC/MS instru- ment using the electrospray ionization. The com- position of hydrochloride salts was determined by the acid-base titration method. Melting points were measured in open capillary tubes and were given uncorrected. All starting compounds and solvents were obtained from Enamine Ltd. and used without additional purification. The general procedure for the Sonoga- shira reaction (compounds 2a – g) To the solution of 1a – g (100 g) in 1.0 L dioxa- ne, TMS-acetylene (1.2 equiv.) and TEA (4.0 equiv.) were was added. Then the mixture was degassed under argon and stirred for 10 min, CuI (0.05 equiv.) and Pd(dppf)Cl2 (0.03 equiv.) were added in one portion under the argon atmosphere, the result- ing mixture was stirred at 90 °C for 16 h. Upon completion of the reaction, the mixture was fil- tered through a celite pad and concentrated un- der vacuum. The crude mixture was purified by flash column chromatography in the correspond- ing eluent described below to give pure 2a – g. 3-((Trimethylsilyl)ethynyl)pyrazin-2-amine (2a) Flash chromatography purification using CHCl3–MeCN mixture (9:1) as an eluent. A yellow solid. Yield – 100.8 g (68.2 %). M. p. 115 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.24 (9H, s), 6.48 (2H, s), 7.72 (1H, d, J = 2.5Hz), 7.93 (1H, d, J = 2.2Hz). 13C NMR (126 MHz, DMSO-d6), δ, ppm: -0.4, 100.1, 100.8, 122.9, 132.5, 142.2, 156.3. LCMS (ES-API), m/z 192 [M+H]+. HRMS (APCI), m/z: calcd for C9H13N3Si 191.0879, found 191.0875. 2-Methyl-5-((trimethylsilyl)ethynyl)pyrimi- din-4-amine (2b) Flash chromatography purification using CHCl3 as an eluent. A white solid. Yield – 81.2 g (74.4 %). M. p. 125 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.21 (9H, s), 2.31 (3H, s), 7.46 (2H, br. s), 8.12 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: -0.2, 25.5, 97.5, 98.0, 102.2, 157.9, 162.9, 166.1. LCMS (ES-API), m/z 206 [M+H]+. HRMS (APCI), m/z: calcd for C10H15N3Si 205.1030, found 205.1035. 2-Chloro-5-((trimethylsilyl)ethynyl)pyridin- 4-amine (2c) Flash chromatography purification using CHCl3 as an eluent. A yellow solid. Yield – 69.7 g (64.3 %). M. p. 108 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 7.93 (1H, s), 6.63 (1H, s), 6.58 (2H, br. s), 0.22 (9H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 0.4, 98.5, 103.1, 103.5, 106.8, 150.6, 152.4, 157.0. LCMS (ES-API), m/z: 225 [M+H]+. 2-Methoxy-3-((trimethylsilyl)ethynyl)pyridin- 4-amine (2d) The reaction mixture was stirred at 60° C for 16 h. Flash chromatography purification using CHCl3 as an eluent. A yellow solid. Yield – 67.6g (76.7 %). M. p. 72 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.20 (9H, s), 3.77 (3H, s), 6.09 (2H, br. s), 6.32 (1H, d, J = 6.0 Hz), 7.60 (1H, d, J = 6.0 Hz). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 0.6, 53.6, 88.0, 98.1, 104.0, 104.5, 145.9, 157.8, 164.6. LCMS (ES-API), m/z: 221 [M+H]+. HRMS (APCI), m/z: calcd for C11H16N2OSi 220.1032, found 220.1026. 6-(Trifluoromethyl)-2-((trimethylsilyl)ethy- nyl)pyridin-3-amine (2e) Flash chromatography purification using CHCl3 as an eluent. A white solid. Yield – 102.3 g (77.9 %). M. p. 110 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.25 (9H, s), 6.16 (2H, s), 7.21 (1H, d, J = 8.5Hz), 7.49 (1H, d, J = 8.5Hz). 13C NMR (126 MHz, DMSO-d6), δ, ppm: -0.3, 99.8, 100.6, 120.4, 121.4, 125.5, 133.7, 134.0, 148.5. 19F NMR (376 MHz, DMSO-d6), δ, ppm: -65.35. LCMS (ES-API), m/z: 259 [M+H]+. HRMS (APCI), m/z: calcd for C11H13F3N2Si 258.0798, found 258.0800. 5-(Trifluoromethyl)-2-((trimethylsilyl)ethy- nyl)pyridin-3-amine (2f) Flash chromatography purification using CHCl3 as an eluent. ISSN 2308-8303 (Print) / 2518-1548 (Online) 7 Journal of Organic and Pharmaceutical Chemistry 2025, 23 (3) A white solid. Yield – 91.2 g (70.2 %). M. p. 132 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.26 (9H, s), 5.94 (2H, s), 7.37 (1H, s), 8.01 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: -0.4, 100.2, 101.7, 116.6, 122.5, 124.7, 129.4, 132.9, 146.0. 19F NMR (376 MHz DMSO-d6), δ, ppm: -61.99. LCMS (ES-API), m/z: 259 [M+H]+. HRMS (APCI), m/z: calcd for C11H13F3N2Si 258.0804, found 258.0800. 4-Methyl-2-((trimethylsilyl)ethynyl)pyridin- 3-amine (2g) The crude mixture was treated with MTBE. A gray solid. Yield – 90.8 g (83.2 %). M. p. 121 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 0.24 (9H, s), 5.13 (2H, s), 6.97 (1H, d, J = 4.6 Hz), 7.66 (1H, d, J = 4.3 Hz). 13C NMR (126 MHz, DMSO-d6), δ, ppm: -0.2, 17.0, 98.7, 102.0, 125.3, 125.7, 129.7, 138.0, 144.8. LCMS (ES-API), m/z: 205 [M+H]+. HRMS (APCI), m/z: calcd for C11H16N2Si 204.1083, found 204.1089. The general procedure for heterocycli- zation 3a – g KOtBu (1.2 equiv.) was added in one por- tion to a stirring solution of compound 2a – g (1 equiv., 50 g) in 1.0 L THF at 0 °C. The tem- perature was brought to reflux, and the result- ing mixture was stirred for 15 h. After that, the solvent was evaporated to dryness, the residue was poured into the mixture of the concentrat- ed HCl and water (100 mL–400 mL), the mix- ture was stirred for 30 min and filtered through celite; the mother liquid was neutralized with ammonia to pH = 10, stirred for another 30 min. Then the precipitate was collected via the vacu- um filtration. In case if the precipitate was not formed, the mixture was extracted with DCM (3×200 mL), combined organic layers were dried with the anhydrous Na2SO4 and concentrated. Compounds 3a – g required no additional puri- fication. 5H-Pyrrolo[2,3-b]pyrazine (3a) A white solid. Yield – 17.2 g (55.2 %). M. p. 153 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 6.61 (1H, dd, J = 3.5, 1.7 Hz), 7.85 (1H, t, J = 3.2 Hz), 8.21 (1H, d, J = 2.6 Hz), 8.36 (1H, d, J = 2.3 Hz), 12.03 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 100.8, 131.5, 137.1, 138.5, 139.6, 141.7. LCMS (ES-API), m/z: 120 [M+H]+. HRMS (APCI), m/z: calcd for C6H5N3Si 119.0492, found 119.0483. 2-Methyl-7H-pyrrolo[2,3-d]pyrimidine (3b) A white solid. Yield – 18.4 g (56.8 %). M. p. 179 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 2.60 (3H, s), 6.49 (1H, d, J = 2.6Hz), 7.42 (1H, s), 8.85 (1H, s), 11.88 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 25.9, 99.6, 116.0, 126.8, 149.2, 152.4, 159.73. LCMS (ES-API), m/z: 134 [M+H]+. HRMS (APCI), m/z: calcd for C7H7N3 133.0644, found 133.0640. 6-Chloro-1H-pyrrolo[3,2-c]pyridine (3c) A brown solid. Yield – 45 g (73.7 %). M. p. 189 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 6.59 (1H, m), 7.42 (1H, s), 7.48 (1H, m), 8.60 (1H, s), 11.62 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 101.0, 106.4, 125.0, 128.7, 141.7, 141.8, 142.5. LCMS (ES-API), m/z: 153 [M+H]+. HRMS (APCI), m/z: calcd for C7H5ClN2 152.0139, found 152.0141. 4-Methoxy-1H-pyrrolo[3,2-c]pyridine (3d) A brown solid. Yield – 37.7 g (56.1 %). M. p. 139 °C. 1H NMR (400 MHz, CDCl3), δ, ppm: 4.10 (3H, s), 6.66 (1H, d, J = 2.3Hz), 6.97 (1H, d, J = 5.7 Hz), 7.13 (1H, m), 7.84 (1H, d, J = 5.7 Hz), 8.59 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 52.9, 99.5, 103.2, 112.1, 124.7, 137.4, 141.5, 157.7. LCMS (ES-API), m/z: 149 [M+H]+. HRMS (APCI) m/z: calcd for C8H8N2O 148.0637, found 148.0637. 5-(Trifluoromethyl)-1H-pyrrolo[3,2-b]pyridi- ne (3e) A white solid. Yield – 30.5 g (78.2 %). M. p. 213 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 6.7 (1H, s), 7.54 (1H d, J = 8.2 Hz), 7.88 (1H, s), 7.99 (1H, d, J = 8.5 Hz), 11.76 (1H, br). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 102.0, 112.5, 119.4, 121.7 – 123.8 (q, J = 265 Hz, CF3), 129.6, 132.3, 139.4, 145.7. 19F NMR (376 MHz, DMSO-d6) δ -64.47 LCMS (ES-API), m/z: 187 [M+H]+. HRMS (APCI), m/z: calcd for C8H5F3N2 186.0402, found 186.0405. 6-(trifluoromethyl)-1H-pyrrolo[3,2-b]pyridine (3f) A white solid. Yield – 29.2 g (74.9 %). M. p. 190 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 6.71 (1H, s), 7.95 (1H, s), 8.16 (1H, s), 8.65 (1H, s), 11.85 (1H, br). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 101.9, 117.3, 117.4, 124.5 – 126.3 (q, J = 227 Hz, CF3), 128.1, 134.7, 138.4, 147.8. 19F NMR (376 MHz, DMSO-d6) δ -58.81. LCMS (ES-API), m/z: 187 [M+H]+. HRMS (APCI), m/z: calcd for C8H5F3N2 186.0406, found 186.0405. Methyl-1H-pyrrolo[3,2-b]pyridine (3g) A brown solid. Yield – 21.7 g (67.0 %) M. p. 189 °C. 1H NMR (400 MHz, DMSO-d6), δ, ppm: 2.48 (3H, s), 6.51 (1H, s), 6.89 (1H, s), 7.57 (1H, s), 8.17 (1H, s), 11.35 (1H, s). 13C NMR (126 MHz, DMSO-d6), δ, ppm: 16.2, 101.8, 117.4, 128.3, 128.9, 142.3, 145.2, 145.6. LCMS (ES-API) m/z: 133 [M+H]+. HRMS (APCI), m/z: calcd for C8H8N2 132.0685, found 132.0687. ISSN 2308-8303 (Print) / 2518-1548 (Online) 8 Журнал органічної та фармацевтичної хімії 2025, 23 (3) The procedure for the preparation of me- thyl 1H-pyrrolo[3,2-c]pyridine-6-carboxyla- te (4c) To the solution of compound 3c (30 g, 0,196 mol) and TEA (32.9 mL, 0.234 mol) in 400 mL MeOH in 500 mL autoclave, Pd(dppf)Cl2 (4.75 g, 0.006 mol) was added. The reaction vessel was flushed three times with CO gas and stirred under 20 atm at 120 °C for 16 h. Upon completion, the reaction mixture was cooled to room temperature, and the precipitate was collected via the vacuum filtra- tion, washed with water and MTBE, then dried in air to obtain a pure product 4c (27.3 g, 78.9 %). A yellow solid. Yield – 27.3 g (78.9 %). M. p. 183 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 3.85 (3H, s), 6.70 (1H, d, J = 3.2 Hz), 7.62 – 7.73 (1H, m), 8.15 (1H, s), 8.89 (1H, s), 11.94 (1H, s). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 52.4, 101.5, 110.0, 127.3, 130.4, 138.6, 139.2, 143.0, 166.8. LCMS (ES), m/z: 177 [M+H]+. HRMS (APCI), m/z: calcd for C9H8N2O2 176.0586, found 176.0581. The procedure for the preparation of me- thyl 1H-pyrrolo[3,2-c]pyridine-6-carboxyla- te (5c) To a cooled solution of LiAlH4 (14.25 g, 1.25 equiv.) in THF (1 L) at 0 °C, 4c (53.0 g, 0.30 mol) was added portionwise, keeping temperature bellow 0 °C. Then mixture was stirred at room tempe- rature for 15 h. Upon completion, the reaction mixture was cooled to 0 oC and carefully neutra- lized with the water-NaOH solution and water. The mixture was stirred for 1 h at room temper- ature, and the precipitate was filtered through celite, washed with MTBE, then the mother liquid was evaporated in vacuo to give a pure product 5c (31.3 g, 70.2 %) A yellow solid. Yield 31.3 g (70.2 %). M. p. 132 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 4.26 (s, 2H), 5.27 (1H, br. s), 6.51 (1H, s), 7.37 (1H, s), 7.42 (1H, s), 8.69 (1H, s), 11.44 (1H, s). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 65.0, 100.6, 103.1, 123.9, 126.7, 140.7, 142.2, 153.1; LCMS (ES), m/z: 149 [M+H]+. HRMS (APCI), m/z: calcd for C8H8N2O 148.0637, found 148.0635. The procedure for the preparation of 1H- pyrrolo[3,2-c]pyridin-6-yl)methanol (6c) To the mixture of 5c (20.0 g, 0.135 mol) in 400 mL of EtOAc, IBX (1.5 equiv.) was added in one portion. Then the mixture was stirred at reflux for 15 h. Upon completion, the reaction mixture was filtered hot through celite, washed with EtOAc, then the mother liquid was washed with the K2CO3 water solution (20 g in 500 mL of water), the organic phase was dried and evapo- rated in vacuo to give a pure product 6c (10.4 g, 52.7 %). A yellow solid. Yield – 10.4 g (52.7 %). M. p. 162 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 6.73 (1H, d, J = 2.5 Hz), 7.75 (1H, d, J = 3Hz), 8.01 (1H, s), 9.01 (1H, s), 10.05 (1H, s), 12.08 (1H, s). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 101.3, 106.6, 127.9, 131.0, 138.6, 143.2, 144.8, 193.6. GCMS, m/z: 146 [M]+; HRMS (APCI), m/z: calcd for C8H6N2O 146.0476, found 146.0480. The procedure for the preparation of 1H- pyrrolo[3,2-c]pyridine-6-carboxylic acid hyd- rochloride (7c) To the solution of compound 4c (1.0 g, 0.0057 mol), the conc. HCl (10 mL) was added. The resulting mixture was stirred at 80 °C for 15 h. Upon com- pletion, the reaction mixture was evaporated to dryness to obtain a yellow solid product 7c in the form of HCl salt (1.04 g, 92.0 %). A yellow solid. Yield – 1.04 g (92 %). M. p. 280 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 7.15 (1H, s), 8.12 (1H, s), 8.49 (1H, s), 9.29 (1H, s), 13.81 (1H, s), 14.80 (1H, br). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 105.9, 111.3, 126.0, 130.9, 135.2, 137.8, 141.6, 162.3. LCMS (ES), m/z: 163 [M+H]+. HRMS (APCI) m/z: calcd for C8H6N2O2 162.0428, found 162.0429. The procedure for the preparation of 6-(chloromethyl)-1H-pyrrolo[3,2-c]pyridine hydrochloride (8c) To the solution of SOCl2 (1.5 equiv.) in 400 mL of CHCl3, alcohol 5c (30 g, 0.20 mol) was added dropwise at 0 °C. Then the mixture was stirred at room temperature for 16 h. Upon completion, the precipitate was collected via vacuum filtra- tion, washed with CHCl3, then dried to obtain pure product 8c (30.5 g, 74.2 %, hydrochloride salt). A yellow solid. Yield – 30.5 g (74.2 %). M. p. 209 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 5.20 (2H, s), 7.01 (1H, d, J = 0.5 Hz), 7.96 (1H, d, J = 2.2Hz), 8.12 (1H, s), 9.27 (1H, s), 13.37 (1H, s), 15.86 (1H, br. s). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 41.5, 104.8, 110.1, 124.1, 133.6, 136.8, 139.7, 142.4. LCMS (ES), m/z: 167 [M+H]+. HRMS (APCI) m/z: calcd for C8H7ClN2 166.0297, found 166.0298. The procedure for the preparation of 6-(azidomethyl)-1H-pyrrolo[3,2-c]pyridine (9c) To a cooled to 0 °C solution of DBU (1.2 equiv.) and 5c (5.0 g, 0.03 mol) in 200 mL of THF, DPPA (1.2 equiv.) was added portionwise keeping tem- perature bellow 0 °C. Then the mixture was ISSN 2308-8303 (Print) / 2518-1548 (Online) 9 Journal of Organic and Pharmaceutical Chemistry 2025, 23 (3) stirred at room temperature for 15 h. Upon com- pletion, the reaction mixture was evaporated to dryness. The crude mixture was purified by co- lumn chromatography using the CHCl3-MeCN system as an eluent to give 9c (2.5 g, 42.8 %) as a yellow solid with 80 % purity. The product was used in the next step without any purification due to stability issues. Yield – 2.5 g (42.8 %). Purity 80 %. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 4.50 (2H, s), 6.58 (1H, d, J = 2.8 Hz), 7.41 – 7.52 (2H, m), 8.82 (1H, s), 11.66 (1H, s). The procedure for the preparation of (1H-pyrrolo[3,2-c]pyridin-6-yl)methanami- ne (10c) To the solution of crude 9c (2.5 g, 0.01 mol) in 50 mL of THF, PPh3 (1.2 equiv.) was added in one portion and H2O (1.5 equiv.) in 30 min. The resulting mixture was stirred at room tem- perature for 15 h. Upon completion, a diluted HCl (2 equiv.) was added, the water solution was ex- tracted twice with CHCl3 (for PPh3 and Ph3PO separation), and then the water solution was neutralized with K2CO3. The precipitate was collected via the vacuum filtration, washed with THF, then dried to obtain a pure product 10c (2.0 g, 94.3 %). A white solid. Yield – 2.0 g (94.3  %). M. p. 190 °C. 1H NMR (500 MHz, DMSO-d6), δ, ppm: 1.96 – 2.40 (1H, br. s), 3.85 (2H, s), 6.52 (1H, d, J = 2.3 Hz), 7.37 (1H, d, J = 2.0 Hz), 7.39 (1H, s), 8.72 (1H, s), 11.45 (1H, br. s). 13C NMR (151 MHz, DMSO-d6), δ, ppm: 48.0, 100.5, 103.6, 123.8, 126.6, 140.7, 142.3, 154.0. LCMS (ES), m/z: 148 [M+H]+. 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Information about the authors: Mykyta V. Kordubailo (corresponding author), Ph.D. student, Medicinal Chemistry Department, Institute of Organic Chemistry of the National Academy of Sciences of Ukraine; https://orcid.org/0000-0002-8567-9838; e-mail for correspondence: nikita141193@gmail.com. Andrey A. Tolmachev, D.Sci. in Chemistry, Professor, Director of ChemBioCenter of Taras Shevchenko National University of Kyiv; https://orcid.org/0009-0001-4351-2829.
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spelling oai:ojs.journals.uran.ua:article-3233072026-08-22T19:32:42Z Optimization and Scaling up of the Azaindole Derivatives Synthesis Оптимізація та масштабування методу синтезу похідних азаіндолу Kordubailo, Mykyta V. Tolmachev, Andrey A. азаіндоли реакція Соногашіри синтез Ларока карбонілювання azaindoles Sonogashira coupling Larock synthesis carbonylation In this study, an optimized method for the synthesis of azaindoles was developed and successfully scaled up to a 100 g batch. Improved yields were observed when using electron-deficient azaheterocycles and substrates bearing electron-withdrawing substituents. 6-Chloro-1H-pyrrolo[3,2-c]pyridine was selected for further functionalization using a carbonylation protocol involving carbon monoxide. As a result, novel and promising building blocks for medicinal chemistry were obtained. У цьому дослідженні було розроблено оптимізований метод синтезу азаіндолів, який успішно масштабовано для одержання до 100 г цільової сполуки. Кращі виходи спостерігались у разі використання електронодефіцитних азагетероциклів та замісників з електронно-акцепторними властивостями. Для подальшої функціоналізації було обрано 6-хлоро-1H-піроло[3,2-c]піридин шляхом його карбонілювання дією карбон(ІІ) оксиду. Як результат було одержано нові перспективні будівельні блоки для потреб медичної хімії. National University of Pharmacy 2025-11-21 Article Article application/pdf application/pdf https://ophcj.nuph.edu.ua/article/view/323307 10.24959/ophcj.25.323307 Journal of Organic and Pharmaceutical Chemistry; Vol. 23 No. 3 (2025); 4-10 Журнал органической и фармацевтической химии; Том 23 № 3 (2025); 4-10 Журнал органічної та фармацевтичної хімії; Том 23 № 3 (2025); 4-10 2518-1548 2308-8303 en https://ophcj.nuph.edu.ua/article/view/323307/331397 https://ophcj.nuph.edu.ua/article/view/323307/331451 Copyright (c) 2025 Mykyta V. Kordubailo, Andrey A. Tolmachev http://creativecommons.org/licenses/by/4.0
spellingShingle азаіндоли
реакція Соногашіри
синтез Ларока
карбонілювання
Kordubailo, Mykyta V.
Tolmachev, Andrey A.
Оптимізація та масштабування методу синтезу похідних азаіндолу
title Оптимізація та масштабування методу синтезу похідних азаіндолу
title_alt Optimization and Scaling up of the Azaindole Derivatives Synthesis
title_full Оптимізація та масштабування методу синтезу похідних азаіндолу
title_fullStr Оптимізація та масштабування методу синтезу похідних азаіндолу
title_full_unstemmed Оптимізація та масштабування методу синтезу похідних азаіндолу
title_short Оптимізація та масштабування методу синтезу похідних азаіндолу
title_sort оптимізація та масштабування методу синтезу похідних азаіндолу
topic азаіндоли
реакція Соногашіри
синтез Ларока
карбонілювання
topic_facet азаіндоли
реакція Соногашіри
синтез Ларока
карбонілювання
azaindoles
Sonogashira coupling
Larock synthesis
carbonylation
url https://ophcj.nuph.edu.ua/article/view/323307
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