Abstract
An approach to rel-(4aS,6R,7aR)-octahydro-1H-cyclopenta[b]pyridine-6-carboxylic acid—a bicyclic conformationally restricted γ-aminobutyric acid (GABA) analogue was developed. The eight-step sequence relied on the reaction of 2,3-bis(chloromethyl)pyridine and a C1-binucleophile and the catalytic reduction of the pyridine ring as the key steps and allowed for the preparation of the title compound in 9.0% overall yield. Assessment of the octahydro-1H-cyclopenta[b]pyridine scaffold geometry showed that this template can be considered truly three-dimensional.
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Introduction
Conformational restriction is a tool which is widely used in different areas of chemistry, especially those related to molecular interactions with biological macromolecules. It is recognized that conformationally restricted molecules have advantages with respect to their potency and selectivity towards biological targets as compared to their flexible counterparts (Mann 2008; Fang et al. 2014). Compounds with reduced conformational flexibility—analogs of natural compounds are of special interest to bioorganic and medicinal chemistry, and of these, conformationally restricted amino acids have attracted most interest over the last two decades (Vagner et al. 2008; Janecka and Kruszynski 2005; Komarov et al. 2004; Gellman 1998; Soloshonok 2002; Cativiela and Ordóñez 2009; Trabocchi et al. 2008; Sorochinsky et al. 2013a, b; Aceña et al. 2014; Fülöp et al. 2006; Kiss et al. 2015; Wang et al. 2017). γ-Aminobutyric acid (GABA, 1), which is a chief neurotransmitter in mammalian, is an attractive target for molecular design based on reducing conformational flexibility (Fig. 1) (Ordóñez and Cativiela, 2007). Conformationally restricted GABA analogues (e.g, 2–4) were used in the studies of various GABA-related biological activities such as GABA receptors binding, GABA uptake or GABA aminotransferase inhibition (Witiak et al. 1986; Crittenden et al. 2006; Pingsterhaus et al. 1999; Mortensen et al. 2004; Chebib et al. 2001; Kobayashi et al. 2014).
In this work, we report the synthesis of novel bicyclic conformationally restricted GABA analogue, octahydro-1H-cyclopenta[b]pyridine-6-carboxylic acid (5) (Fig. 2). Notably, derivatives of octahydro-1H-cyclopenta[b]pyridine have already shown their utility for the design of biologically relevant molecules, e.g., local anesthetic rodocaine (6) (Van Bever et al. 1973), bone resorption inhibitor 7 (Szabo et al. 2002), nitric oxide synthase inhibitor 8 (Guthikonda et al. 2005).
Results and discussion
Our approach to the synthesis of 5 commenced from the dichloride 9, which is known in the literature and can be prepared from commercially available quinolinic acid (10) in three steps (Scheme 1) (Grimm et al. 2002). Construction of the cyclopentane ring was expected to proceed via double alkylation of a C1-binucleophile with 9. Several C1-binucleophiles 11 were tested for that purpose (Table 1). Optimization of the reaction conditions showed that using NaH in DMSO gave the highest yields of the bicyclic adducts as compared to other systems studied, e.g., NaH—DMF or EtONa—EtOH. In the latter case, considerable formation of the products resulting from the side reaction at the 1:2 ratio of 9 and the corresponding binucleophile was observed according to 1H NMR and LC–MS. Variation of the structure of C1-binucleophile revealed that the yield of the target product 12 depended strongly on the pKa value of the corresponding CH-acid (Bordwell 1988). The best results were obtained with malonic acid derivatives (pKa = 11–17); the corresponding bicyclic adducts 12c–f were isolated and characterized.
The product 12e obtained from diethyl malonate was subjected to acidic hydrolysis, leading to the carboxylic acid 13 (isolated as a hydrochloride in 90% yield). Surprisingly, hydrogenation of 13 obtained by this method did not give reproducible results; the rate of the reaction and the diastereomeric ratio varied significantly, possibly due to the poisoning of the catalyst by traces of sulfur which remained in the sample of 13 even after the chromatographic purification. We have used another sample of 13, which was obtained from the batch of 12 prepared via alkylation of diethyl malonate by 9 over NaH in DMF instead of DMSO. Although the yield of 12 prepared by this method was slightly lower (65%), in this case, hydrogenation over Pd(OH)2-C was successful and gave the corresponding methyl ester 14 as ca. 85:15 mixture of stereoisomers (according to 1H NMR). All attempts to separate this mixture were unfruitful; therefore, it was used in the next step without characterization. Moreover, chromatographic separation of the corresponding acetyl, Boc, and Cbz derivatives also was not successful. We have then prepared the p-nitrobenzoyl derivative of 14, aiming at its purification by recrystallization. Although the recrystallization was not fruitful, the rel-(4aS,6R,7aR) diastereomer 15 could be isolated in a pure form after column chromatography (52% yield from 13). Its relative stereochemistry was established using X-Ray diffraction studies with the corresponding carboxylic acid 16, prepared by alkaline hydrolysis of 15 (Fig. 3). Acidic hydrolysis of 15 gave the target amino acid hydrochloride 17 in 62% yield.
Analysis of the 1,6-disubstituted octahydro-1H-cyclopenta[b]pyridine scaffold geometry using the exit vector plot (EVP) tool (Grygorenko et al. 2016, 2018) (applied to the X-Ray diffraction study data for 16) showed that this bicyclic template can be considered as truly three-dimensional (Fig. 4). The main idea behind the EVP tool is based on simulation of the two functional groups attached to the scaffold by exit vectors. Relative spatial orientation of these vectors is then described by four geometric parameters (r, φ1, φ2, and θ). These parameters can discriminate various spatial arrangements of the exit vectors, i.e., linear (φ1/φ2 ~ 0°), flattened (θ ~ 0/180°), and three-dimensional (φ1/φ2 and θ are far from the aforementioned values). In the case of 16, the corresponding values were r = 3.75 Å, φ1 = 46°, φ2 = 49°, and θ = 134°. These data show that the title scaffold is larger than the common saturated rings [e.g., for the compounds 2 ((a) Kaneda et al. 1980; Woll et al. 2001) and 3 (Mora et al. 2005), the corresponding data points are located in the typical α–ε areas of EVPs] and falls into the three-dimensional category. It should be noted that the φ1/φ2—θ plot (Fig. 4b) demonstrates some geometrical similarity between the 1,6-disubstituted rel-(4aS,6R,7aR)-octahydro-1H-cyclopenta[b]pyridine and trans-1,3-disubstituted cyclopentane scaffolds (in 16 and a peptidomimetic derived from trans-2, respectively).
Conclusions
An approach to the synthesis of novel conformationally restricted GABA analogues based on octahydro-1H-cyclopenta[b]pyridine scaffold was developed. This amino acid can be used in the studies of various GABA-related biological activities, and also as a three-dimensional building block for design of lead-oriented compound libraries in drug discovery.
Materials and methods
General
The solvents were purified according to the standard procedures. All starting materials were obtained from Enamine Ltd. Analytical TLC was performed using Polychrom SI F254 plates. Column chromatography was performed using Kieselgel Merck 60 (230–400 mesh) as the stationary phase. 1H, 13C, and 19F NMR spectra were recorded on a Bruker 170 Avance 500 spectrometer (at 500 MHz for Protons and 126 MHz for Carbon-13) and Varian Unity Plus 400 spectrometer (at 400 MHz for protons, 101 MHz for Carbon-13, and 376 MHz for Fluorine-19). Tetramethylsilane (1H, 13C) or C6F6 (19F) were used as standards. Elemental analyses were performed at the Laboratory of Organic Analysis, Institute of Organic Chemistry, National Academy of Sciences of Ukraine, their results were found to be in good agreement (± 0.4%) with the calculated values. Mass spectra were recorded on Agilent 1100 LCMSD SL instrument [chemical ionization (APCI)] and Agilent 5890 Series II 5972 GCMS instrument [electron impact ionization (EI)].
General procedure for the preparation of 12c–f
Sodium hydride (60% in mineral oil) (600 mg, 15 mmol) was suspended in DMSO (50 mL), and the compound 11 (4.7 mmol) was added upon vigorous stirring. The resulting mixture was stirred for additional 10 min, and 2,3-bis(chloromethyl)pyridine hydrochloride (9·HCl) (1 g, 4.7 mmol) was added. The resulting mixture was stirred at 50 °C overnight, then cooled, and ice-cold H2O (50 mL) was added. The mixture was extracted with Et2O (3 × 15 mL), the combined organic extracts were dried over Na2SO4 and evaporated in vacuo. The crude product was purified by column chromatography (EtOAc—Hexanes (2:1) as eluent).
5,7-Dihydro-6H-cyclopenta[b]pyridine-6,6-dicarbonitrile (12c)
Yield 64 mg (72%). Yellowish solid. Mp 109–112 °C. Anal. Calcd. for C10H7N3 C 70.99, H 4.17, N 24.84. Found C 70.62, H 4.45, N 25.04. MS (EI): 169 (M+), 168 (M+–H), 143 (M+–CN), 142 (M+–HCN). 1H NMR (500 MHz, CDCl3) δ 8.56 (d, J = 4.2 Hz, 1H), 7.66 (d, J = 7.6 Hz, 1H), 7.30–7.25 (dd, J = 7.6, 4.2 Hz, 1H), 3.86 (s, 2H), 3.81 (s, 2H). 13C NMR (126 MHz, CDCl3) δ 171.2, 161.1, 148.4, 133.3, 132.0, 121.7, 41.7, 38.3, 29.6.
Ethyl 6-cyano-6,7-dihydro-5H-cyclopenta[b]pyridine-6-carboxylate (12d)
Yield 64 mg (68%). Yellowish oil. Anal. Calcd. for C12H12N2O2 C 66.65, H 5.59, N 12.95. Found C 66.38, H 5.37, N 13.33. MS (EI): 216 (M+), 189 (M+–HCN), 143 (M+–CO2Et). 1H NMR (500 MHz, DMSO-d6) δ 8.48 (d, J = 4.6 Hz, 1H), 7.71 (d, J = 7.5 Hz, 1H), 7.29 (dd, J = 7.3, 4.6 Hz, 1H), 4.31 (q, J = 7.1 Hz, 2H), 3.86 (d, J = 17.0 Hz, 1H), 3.78 (d, J = 17.0 Hz, 1H), 3.75 (d, J = 15.8 Hz, 1H), 3.63 (d, J = 15.8 Hz, 1H), 1.34 (t, J = 7.1 Hz, 3H). 13C NMR (126 MHz, CDCl3) δ 167.8, 158.0, 147.2, 134.4, 133.2, 123.2, 119.6, 63.7, 45.3, 43.5, 40.9, 13.9.
Diethyl 5,7-dihydro-6H-cyclopenta[b]pyridine-6,6-dicarboxylate (12e)
Yield 6.60 g (77%).Yellowish oil. Anal. Calcd. for C14H17NO4 C 63.87, H 6.51, N 5.32. Found C 64.17, H 6.31, N 5.65. MS (EI): 263 (M+), 189, 117. 1H NMR (400 MHz, CDCl3) δ 8.35 (d, J = 4.9 Hz, 1H), 7.47 (d, J = 7.2 Hz, 1H), 7.05 (dd, J = 7.2, 4.9 Hz, 1H), 4.20 (q, J = 7.1 Hz, 4H), 3.67 (s, 2H), 3.57 (s, 2H), 1.24 (t, J = 7.1 Hz, 6H). 13C ЯMP (126 MHz, CDCl3), δ 171.2, 161, 148.4, 133.3, 132, 121.7, 61.9, 41.7, 38.3, 22.7, 14.0.
Diisopropyl 5,7-dihydro-6H-cyclopenta[b]pyridine-6,6-dicarboxylate (12f)
yield 75 mg (55%). Yellowish solid. Mp 87–89 °C. Anal. Calcd. for. C16H21NO4 C 65.96, H 7.27, N 4.81. Found C 65.63, H 6.98, N 5.14. MS (CI): 292 (MH+). 1H NMR (500 MHz, CDCl3) δ 8.37 (d, J = 4.8 Hz, 1H), 7.48 (d, J = 7.5 Hz, 1H), 7.06 (dd, J = 7.5, 4.8 Hz, 1H), 5.06 (sept, J = 6.2 Hz, 2H), 3.67 (s, 2H), 3.56 (s, 2H), 1.24 (d, J = 6.2 Hz, 12H). 13C NMR (126 MHz, CDCl3) δ 170.8, 161.2, 148.4, 133.4, 132.0, 121.7, 69.4, 58.0, 41.7, 38.2, 21.5.
Diethyl 5,7-dihydro-6H-cyclopenta[b]pyridine-6,6-dicarboxylate (12e) (alternative method)
The procedure was essentially the same as the general method described above, except DMF was used as the solvent instead of DMSO. Yield 24.7 g, 65%.
6,7-Dihydro-5H-cyclopenta[b]pyridine-6-carboxylic acid, hydrochloride (13)
The diester 12e (10.0 g, 3.8 mmol) was dissolved in concentrated aq HCl (10 mL), and the mixture was refluxed for 24 h, then cooled and evaporated to dryness, the residue was treated with Et2O and filtered to give 13. Yield 6.81 g (90%). Greyish solid. Mp 162–166 °C (dec.). Anal. Calcd. for. C9H10ClNO2 C 54.15, H 5.05, Cl 17.76, N 7.02. Found C 53.94, H 5.39, Cl 17.46, N 6.67. MS (CI): 164 (MH+), 118 (M+–COOH). 1H NMR (500 MHz, D2O) δ 8.41 (d, J = 6.2 Hz, 1H), 8.30 (d, J = 7.6 Hz, 1H), 7.72 (dd, J = 7.6, 6.2 Hz, 1H), 3.69–3.61 (m, 1H), 3.56 (d, J = 7.8 Hz, 2H), 3.47 (dd, J = 17.3, 9.2 Hz, 1H), 3.36 (dd, J = 17.3, 6.5 Hz, 1H). 13C NMR (126 MHz, D2O) δ 177.7, 142.7, 142.4, 138.3, 131.9, 125.1, 41.2, 33.9, 33.7.
rel-(4aS,6R,7aR)-Methyl 1-(4-nitrobenzoyl)octahydro-1H-cyclopenta[b]pyridine-6-carboxylate (15)
Compound 13 (1.00 g, 5.01 mmol) was dissolved in MeOH (15 mL). 20% Pd(OH)2 on charcoal (50 mg) was added, and the mixture was hydrogenated in an autoclave at 50 bar and 35 °C for 8 h. The catalyst was filtered off, washed with MeOH (5 mL), and the filtrate was evaporated in vacuo to give crude 14. The residue was suspended in CH2Cl2 (25 mL), and triethylamine (1.14 g, 11.3 mmol) was added. The reaction mixture was stirred at rt for 10 min and cooled to 0 °C. 4-Nitrobenzoyl chloride (0.930 g, 5.01 mmol) was added to the reaction mixture. The mixture was stirred at rt overnight, and then diluted with 10% aq citric acid. The organic layer was separated, washed with brine (10 mL), dried over Na2SO4 and evaporated. The residue was purified by column chromatography (hexanes: EtOAc (2:1) as eluent) Yield 0.859 g, 52%. White solid, mp 114–118 °C. Anal. Calcd. for. C17H20N2O5 C 61.44, H 6.07, N 8.43. Found C 61.27, H 5.64, N 8.38. MS (CI): 355 (MNa+), 333 (MH+), 301 (MH+–MeOH), 150 (4-O2NC6H4C≡O+). The compound had double set of broadened signals in the NMR spectra due to some exchange process (possibly rotamers at the amide bond). 1H NMR (500 MHz, DMSO-d6, 80 °C) δ 8.25 (d, J =8.5 Hz, 2H), 7.62 (d, J =8.5 Hz, 2H), 4.75–3.47 (br m, 2H), 3.63 (s, 3H), 2.97 (br s, 1H), 2.84 (br s, 1H), 2.16 (app. q, J =11.6 Hz, 1H), 2.11–1.88 (m, 3H), 1.68–1.53 (m, 3H), 1.44–1.30 (m, 2H). 13C NMR (126 MHz, DMSO-d6, 80 °C) δ 176.2, 168.5, 148.4, 143.7, 128.2, 124.2, 56.7 (br s), 52.0, 40.0 (br s), 39.3, 36.1, 33.1, 28.9, 27.1, 24.6. 13C NMR (101 MHz, CDCl3, rt) δ 176.8 and 176.1, 168.7, 148.2, 142.9, 127.8 and 127.3, 123.9, 59.2 and 53.3, 52.0, 43.2 and 37.2, 39.3 and 39.0, 36.6 and 35.9, 33.2 and 32.6, 29.1 and 27.9, 26.9, 25.2 and 24.4.
rel-(4aS,6R,7aR)-1-(4-Nitrobenzoyl)octahydro-1H-cyclopenta[b]pyridine-6-carboxylic acid (16)
To a solution of 15 (100 mg, 0.300 mmol) in MeOH (2 mL), NaOH (14 mg, 0.35 mmol) in H2O (0.1 mL) was added. The reaction mixture was stirred at rt for 8 h. Then MeOH was evaporated in vacuo, and H2O (2 mL) and CH2Cl2 (1 mL) were added. The layers were separated, and the aqueous layer was acidified with 10% aq HCl to pH 2. The product was extracted with CH2Cl2 (2 × 1 mL). The combined organic layers were dried over Na2SO4 and evaporated in vacuo. Yield 90 mg, 94%. White solid. Mp 124–125 °C. Anal. Calcd. for C16H18N2O5: C, 60.37; H, 5.70; N, 8.80. Found: C, 60.04; H, 6.00; N, 8.77. MS (CI): 341 (MNa+), 319 (MH+) (positive mode), 301 (MH+–H2O); 317 (M–H+) (negative mode). The compound had double set of broadened signals in the NMR spectra due to some exchange process (possibly rotamers at the amide bond). 1H NMR (500 MHz, DMSO-d6, 40 °C) δ 8.26 (d, J = 8.0 Hz, 2H), 7.63 (d, J = 8.0 Hz, 2H), 4.81 (br s, 0.5H), 4.40 (s, 0.5H), 3.72 (s, 0.5H), 3.54–3.13 (m, 1H), 3.08 (br s, 0.5H), 2.87 (br s, 1H), 2.26–1.78 (br m, 4H), 1.59 (br s, 3H), 1.35 (br s, 2H); COOH is exchanged with HDO. 1H NMR (500 MHz, DMSO-d6, 80 °C) δ 8.26 (d, J = 8.0 Hz, 2H), 7.63 (d, J = 8.0 Hz, 2H), 4.84–3.00 (br m, 2H), 3.55–2.87 (br m, 1H), 2.75 (br s, 1H), 2.29–2.08 (br m, 1H), 1.97 (br s, 3H), 1.61 (br s, 3H), 1.37 (br s, 2H); COOH is exchanged with HDO. 13C NMR (126 MHz, DMSO-d6, 80 °C) δ 177.0, 168.4, 148.4, 143.7, 128.2, 124.1, 55.8 (br s), 38.7 (br s), 39.5, 36.2, 33.2, 28.9, 27.1, 24.7. 13C NMR (101 MHz, CDCl3) δ 181.2 and 180.6, 169.0, 148.3, 142.6, 127.7 and 127.4, 123.9, 59.2 and 53.5, 43.4 and 37.1, 39.3, 36.6 and 36.0, 33.1 and 32.5, 28.7 and 27.8, 26.8, 25.2 and 24.5. Final atomic coordinates, geometrical parameters and crystallographic data for the compound 16 have been deposited with the Cambridge Crystallographic Data Centre, 11 Union Road, Cambridge, CB2 1EZ, UK (E-mail: deposit@ccdc.cam.ac.uk; fax: +44 1223 336033) and are available on request quoting the deposition number CCDC 1864063.
rel-(4aS,6R,7aR)-Octahydro-1H-cyclopenta[b]pyridine-6-carboxylic acid, hydrochloride (17)
Compound 15 (200 mg, 0.600 mmol) was suspended in 10% aq HCl (2 mL). The mixture was stirred at 85–90 °C for 16 h, then cooled to rt, and CHCl3 (2 mL) was added. The precipitate was filtered off, and the layers were separated. The aqueous layer was evaporated and dried in vacuo. Yield 77 mg, 62%. White solid, mp 188–190 °C (dec.). Anal. Calcd. for. C9H16ClNO2 C 52.56, H 7.84, Cl 17.24, N 6.81. Found C 52.50, H 7.63, Cl 16.93, N 7.15. MS (CI): 170 (MH+). 1H NMR (400 MHz, D2O) δ = 3.61–3.47 (m, 1H), 3.25–3.12 (m, 1H), 3.06–2.92 (m, 1H), 2.91–2.78 (m, 1H), 2.37–2.18 (m, 2H), 2.17–2.05 (m, 1H), 2.03–1.92 (m, 1H), 1.79–1.52 (m, 5H). 13C NMR (126 MHz, D2O) δ 180.8, 57.5, 42.7, 40.9, 36.8, 31.9, 31.3, 22.0, 17.7.
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The authors thank Prof. Andrey A. Tolmachev for his encouragement and support and Ms. Yuliya Kuchkovska for her help with preparation of Fig. 3.
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The work was funded by Enamine Ltd.
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Melnykov, K.P., Volochnyuk, D.M., Ryabukhin, S.V. et al. A conformationally restricted GABA analogue based on octahydro-1H-cyclopenta[b]pyridine scaffold. Amino Acids 51, 255–261 (2019). https://doi.org/10.1007/s00726-018-2660-1
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DOI: https://doi.org/10.1007/s00726-018-2660-1