Straightforward Synthesis of Thiophene Bioisosteres of the Pyrrolo[3,2-c]quinoline Framework from Martinelline Alkaloids

Abstract

We report the first green and diastereoselective synthesis of novel thiophene bioisosteres designed to mimic the privileged pyrrolo[3,2-c]quinoline core of martinelline alkaloids. The key step features an intramolecular 1,3-dipolar cycloaddition of in situ generated non-stabilized azomethine ylides from sarcosine, which proceeds with excellent yield and diastereoselectivity. This sustainable protocol, leveraging ultrasonic irradiation, recyclable hydrotalcite catalysts, and the green solvent cyclopentyl methyl ether (CPME), efficiently constructs the complex tricyclic framework. The structure and stereochemistry of the novel bioisostere were unambiguously confirmed by X-ray crystallography. This method offers a valuable, eco-friendly approach for diversifying natural product-inspired libraries in medicinal chemistry.

1. Introduction

Diversity-oriented synthesis (DOS), inspired by natural products, has played a pivotal role in generating structurally diverse libraries that enable the investigation of unexplored chemical and biological spaces [1]. Within this context, martinelline and martinellic acid (Figure 1) represent notable examples of bioactive natural products. These potent non-peptidic bradykinin receptor antagonists, possessing mild antibacterial activity and minimal cytotoxicity, display additional interactions with α11-adrenergic and muscarinic receptors [2]. Structurally, both alkaloids feature a rare tricyclic hexahydropyrrolo[3,2-c]quinoline scaffold, originally isolated from the root bark of Martinella iquitosensis, a tropical South American plant.

The unique biological activities and architecture of martinelline alkaloids have inspired extensive synthetic efforts toward their tricyclic core, leading to analogs that exhibit anticancer, hedgehog signaling inhibition, and selective 5-HT₆ antagonistic properties—an emerging therapeutic approach in Alzheimer’s disease [3,4]. Expanding this structural motif, related heterocycles such as thieno-, furo-, and hexahydro-2H-pyrano[3,2-c]quinolines have also been developed, showing diverse pharmacological profiles including antidiabetic, anti-inflammatory, and antitubercular activities [5].

Such structural exploration aligns closely with the principle of bioisosterism, a cornerstone of modern medicinal chemistry aimed at improving biological selectivity and reducing toxicity. In particular, ring bioisosterism involving the replacement of benzene with electron-rich thiophene has proven effective in fine-tuning the physicochemical and pharmacological properties of drug candidates [6,7].

In recent years, the synthesis of these complex alkaloids has increasingly embraced green chemistry approaches, which emphasize environmentally friendly methodologies to minimize hazardous waste and enhance resource efficiency throughout drug discovery and production [8].

To our knowledge, there have been no reports describing the synthesis of thiophene-containing analogs of the partially reduced pyrrolo[3,2-c]quinoline scaffold, which represents the core architecture of martinelline alkaloids. In continuation of our ongoing efforts to develop green synthetic approaches for bioactive heterocycles via intramolecular 1,3-dipolar cycloaddition reactions [9,10], we report herein an environmentally benign and efficient strategy employing in situ generated, non-stabilized azomethine ylides derived from the decarboxylative condensation of α-amino acids (sarcosine) with tethered 2-alkenylaminothiophene-3-carbaldehydes.

The reason for adding the thiophene nucleus is its role as a bioisosteric replacement for the benzene ring in natural martinelline alkaloids, aimed at altering electronic distribution and potentially enhancing receptor-binding profiles. Additionally, designing the cyclohexene part instead of the ester group found in martinelline or martinellic acid was guided by the goal of maintaining the tricyclic scaffold’s rigidity while improving synthetic accessibility and biological stability. Among the synthesized compounds, the N-sulfonyl derivative (Target that synthesized in this work) is a notable example within this series, broadening chemical diversity and providing new insights into the physicochemical properties of thiophene-substituted analogs (Target in this work), as shown in Figure 1.

2. Results and Discussion

The synthesis of the novel pyrrolo[3,2-c]quinoline analog was initiated from ethyl 2-amino-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate (4) [11], as illustrated in Scheme 1. Compound 4 was first subjected to N-sulfonylation using benzenesulfonyl chloride (5) in the presence of Zn–Al hydrotalcite (Zn–Al HT), which served as a recyclable green catalyst under ultrasonic irradiation to afford the corresponding sulfonamide [12]. The resulting N-sulfonyl intermediate was subsequently N-allylated with allyl bromide, catalyzed by Zn–Al HT under the same ultrasonic conditions, yielding the target N-allylated sulfonamide (6) in excellent yield (91%). Reduction of the ester functionality in compound 6 with lithium aluminum hydride (LiAlH₄) in cyclopentyl methyl ether (CPME), a green solvent [9], furnished the corresponding primary alcohol. Oxidation of this alcohol with activated manganese dioxide in CPME led smoothly to the formation of the key aldehyde intermediate (7) in 77% yield, which served as the crucial precursor for subsequent intramolecular cycloaddition steps (Scheme 1).

An intramolecular 1,3-dipolar cycloaddition reaction was carried out with aldehyde 7 with sarcosine (N-methylglycine) in CPME green solvent under ultrasonic irradiation in the presence of MgAl Hydrotalcite as an efficient solid base catalyst [10]. The reaction afforded the novel cycloadduct 8 in excellent yields (93%) (Scheme 1). With this result in hand, the green reaction routes afforded the thiophene analog of the pyrrolo[3,2-c]quinoline core 8 in excellent yields (cf. Experimental part). Noteworthy, the reaction of aldehyde 7 with sarcosine in CPME as a green solvent under ultrasonic irradiation was carried out using two equivalents of sarcosine and 0.1 g of Mg Al HT base catalyst at 75–80 °C, and isolated high yields were obtained (90%). Attempts to perform this reaction at room temperature (R.T.) under ultrasonic irradiation failed to produce any product.

The mechanistic sequence of the intramolecular 1,3-dipolar cycloaddition reaction is illustrated in Scheme 1, where structures A, B, and C represent crucial intermediates in the reaction pathway. Intermediate A forms through the condensation of the key aldehyde 7 with sarcosine, generating a non-stabilized azomethine ylide. This undergoes decarboxylation to afford the reactive species B, which then participates in an intramolecular 1,3-dipolar cycloaddition, leading to the cyclized intermediate C. The progression from A to B and subsequently to C highlights the underlying green synthetic design, with each step contributing to the assembly of the complex pyrrolo[3,2-c]quinoline core observed in the final product 8. This stepwise mechanistic discussion not only clarifies the synthetic logic but also supports the overall efficiency and environmental compatibility of the developed protocol.

The structure of compound 8 was confirmed based on ¹H- and ¹³C-NMR spectroscopic analyses. The reaction afforded diastereoselectively the cis-fused cycloadducts based on the value of the coupling constants for the pyrrolopyridine ring junction protons (J = 6.5 Hz) [13]. The observed J value is in good agreement with cis-fused partially reduced pyrrolo[3,2-c]quinolines. This diastereo-selectivity was also unambiguously ascertained by X-ray crystallographic analysis of compound 8 (Figure 2).

Based on Houk et al. [14] quantum calculation methods for 1,3-dipolar cycloaddition reactions and Hammond postulates [15], we tentatively postulated two early transition states for these 1,3-dipolar cycloaddition reactions (Figure 3). For strong entropy reasons, TS B was disfavored over TS A because the newly formed six-membered ring in TS B has to adopt a higher energy conformation than in TS A.

Our green protocol applied to the synthesis of 8 goes forward quickly at lower temperatures and softer conditions than conventional heating, thanks to ultrasonic irradiation, which saves energy by producing localized, high-energy conditions that significantly speed up reaction rates [16]. Moreover, using hydrotalcite, a recyclable solid base catalyst, afforded several advantages, such as enabling safer synthesis processes without losing efficiency or selectivity, while also minimizing waste and achieving high atom economy relative to homogeneous bases such as triethylamine. This catalyst replaces harmful homogeneous bases. The adjustable basic sites in hydrotalcite enable quick and environmentally friendly synthesis of heterocycles in dipolar cycloaddition [9,10]. By reducing toxicity and enhancing atom economy, hydrotalcite aids in N-sulfonation by supporting clean sulfonamide production with rapid catalyst recovery. This aligns with green chemistry principles. In addition, A safer alternative to traditional ethers such as THF and dioxane, cyclopropenyl methyl ether (CPME) is known as a green solvent due to its low toxicity, minimal peroxide production, and stability under acidic and basic conditions [17]. The sustainable usage of CPME in organic synthesis and other greener chemical processes is further supported by its high boiling point, hydrophobicity, and potential for bio-based production.

3. Materials and Methods

3.1. General

Thin-layer chromatography was executed on Merck 60 GF254 silica gel plates (Merck, Darmstadt, Germany) pre-coated with a fluorescent indicator, with detection carried out using UV irradiation at 254 and 360 nm. The melting points were determined using the Stuart melting point instrument without alterations. Infrared spectra were acquired by the Nicolet iS10 FT-IR spectrometer with a Smart iTR, an advanced, versatile attenuated total reflectance sample accessory from Thermo Fisher Scientific (Madison, WI, USA). A Bruker Avance III 400 spectrometer (9.4 T, 400.13 MHz for ¹H and 100.62 MHz for ¹³C, Fällanden, Switherland) with a 5 mm BBFO probe was employed to obtain NMR spectra at 298 K. Chemical shifts (δ in ppm) are related to internal standards. Mass spectrum was obtained using an Agilent 1100 LC-MSD SL instrument (chemical ionization (APCI), Santa Clara, USA). Elemental analyses were performed with a EuroVector C, H, N, and S analyzer (EA3000 series, Singen, Germany). Sonication was conducted with an Elma Sonicator P30H device (Singen, Germany) operating at an ultrasonic frequency of 37 kHz and a maximum power of 320 W. The bath temperature increased from 25 to 80 °C after 30 min of operation. All reactions were conducted at the specified temperatures, maintained by the addition or removal of water in an ultrasonic bath; the temperature within the reaction vessel ranged from 76 to 79 °C for cycloaddition reactions executed at 80 °C, and from 25 to 32 °C for those N-sulfonation reactions conducted at 25 °C.

Mg Al HT [10] and Zn Al HT [12] catalysts were prepared according to the reported Literature.

3.2. Crystallographic Studies

Crystals were acquired through the gradual evaporation of the organic component solution in acetonitrile. The acquisition of single-crystal X-ray diffraction data for the organic molecule was performed on a Bruker D8 Venture single-crystal X-ray diffractometer (Ettlingen, Germany) at 120 K, utilizing Mo Kα (λ = 0.71073) radiation. The crystal structure was determined using the SHELXT structure solution program and improved with SHELXL, both incorporated in the Olex2 program package. The crystal structure refinement data for C₂₀H₂₄N₂O₂S₂ are included in the whole CIF file (see Supporting Information File). Comprehensive crystallographic data are accessible via the deposition number (CCDC): 1062830. 12 Union Road, Cambridge CB21 EZ, UK (email: datarequest@ccdc.cam.ac.uk).

3.3. Synthesis 1-Methyl-5-(phenylsulfonyl)-2,3,3a,4,5,7,8,9,10,10c-decahydro-1H-benzo[4,5]thieno[2,3-b]pyrrolo[2,3-d]pyridine (8)

Step I: In a 50 mL Erlenmeyer flask, dissolve ethyl 2-amino-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate (4) (225 mg, 1 mmol) in ethanol (15 mL). Then benzene sulfonyl chloride (5) (210 mg, 12 mmol) at R.T. (25 °C) was added to the reaction mixture and was sonicated for 10 min. Subsequently, Zn Al HT hydrotalcite (1 mol%) was introduced, and sonication continued at R.T. for 30 min, as confirmed by TLC, which indicated the absence of the starting material. The reaction mixture was filtered, the filtrate concentrated under reduced pressure, and the residue solid dissolved in ethanol, then recovered by filtration to obtain the pure product. Then the formed product (was taken as it is without further purification) (365 mg, 1 mmol) and allyl bromide (132 mg, 1.1 mmol) in 15 mL ethanol were taken in a 50 mL Erlenmeyer flask, then Zn Al HT (5 mol%) was added, and the reaction was sonicated for 2 h as examined by TLC in which the starting materials was no longer detected by TLC, The reaction mixture was filtered and the filtrate was concentrated in vacuo and the residual solid was taken in ethanol then collected by filtration to give the pure product 6.

¹H NMR (400 MHz, DMSO): δ_H 1.33 (t, 3H, J = 7.2 Hz, CH₃ ester), 1.82–1.85 (m, 4H),2.21–2.25 (m, 4H), 3.67–3.71 (m, 2H, N-CH₂), 4.11 (q, 2H, J = 7.2 Hz, CH₂ ester), 5.13–5.16 (m, 2H, -CH=CH₂), 5.89 (m, 1H, -CH=CH₂), 7.47–7.65 (m, 5H, ArH) ppm; ¹³C NMR (100MHz, DMSO) δ 14.4, 25.2, 28.4, 31.3, 54.7, 62.3, 114.6, 119.8, 126.3, 127.6, 128.7, 132.8, 134.3, 136.1, 138.5, 141.9, 144.6 ppm.

Step II: At R.T., 405 mg of compound 6 (1 mmol) was added to a LiAlH₄ (57 mg, 1.5 mmol) solution in CPME (5 mL). The mixture was then agitated. After 2 h, the reaction was finished, the mixture was cooled to 0 °C, water (10 mL, initially added dropwise, caution), 2M aqueous sodium hydroxide (20 mL), and water (30 mL) were sequentially added with vigorous stirring. The reaction mixture was then filtered through Celite, and the resulting filter cake was washed thoroughly with ethyl acetate. The filtrate was dried with anhydrous magnesium sulfate, and the solvent was removed under reduced pressure. The solid residue was then diluted with ethanol. Recrystallization in ethyl acetate to isolate and purify the product. The product is subjected directly to oxidation with MnO₂ and follows the reported literature [18] to obtain the main precursor in our study (compound 7).

¹H NMR (400 MHz, DMSO): δ_H 1.84–1.87 (m, 4H), 2.23–2.25 (m, 4H), 3.62–3.67 (m, 2H, N-CH₂), 5.12–5.15 (m, 2H, -CH=CH₂), 5.89 (m, 1H, -CH=CH₂), 7.44–7.62 (m, 5H, ArH), 10.12 (s, 1H, CHO) ppm; ¹³C NMR (100MHz, DMSO) δ 25.1, 28.3, 31.3, 54.8, 119.8, 126.2, 127.6, 128.7, 129.9, 132.8, 134.2, 136.6, 138.7, 141.6, 188.0 ppm.

Step III: A mixture of aldehyde 7 (361 mg, 1 mmol) and sarcosine (98 mg, 1.1 mmol) was suspended in CPME (20 mL), and then 1 mol% of MgAl HT was added. The reaction mixture was sonicated at 80 °C for 1 h (TLC monitoring) and filtered while hot to remove the catalyst and any unreacted amino acid. The solvent was distilled under reduced pressure, and the residue was purified by preparative TLC using a 9:1 acetone-methanol mixture as the eluent (R_f = 0.35), yielding 8 as colorless crystals, 349 mg, 90% yield.

mp: 132–134 °C; ¹H NMR (400 MHz, DMSO): δ_H 1.22–1.23 (m, 2H, H-3),1.34–1.35 (m, 1H, H-8),1.49–1.52 (m, 4H),1.59 (m, 4H), 2.29–2.33 (m, 1H), 2.57 (s, 3H, N-CH₃), 2.83–2.86 (m, 2H), 3.88–3.92 (m, 1H), 4.22–4.23 (m, 1H), 7.61–7.65 (m, 2H, ArH), 7.71–7.76 (m, 1H, ArH), 7.79 (d, 2H, J = 6.11 Hz, ArH) ppm; ¹³C NMR (100MHz, DMSO) δ 21.5, 22.7 (C-8), 23.0 (C-9), 25.2 (C-10), 25.5 (C-7), 25.9(C-3), 32.0(C-3a), 35.8 (1-CH3), 51.5 (C-4), 55.3(C-2), 65.9 (C-10c), 118.6, 128.3, 129.7 (C-5a), 132.4 (C-10a), 133.4, 133.9 (C-10b), 137.3, 138.3, 142.2(C-6a) ppm. FT IR (v_max cm⁻¹) 2922, 2853, 1465, 1377, 1238, 1162, 1116, 1097, 1029, 721; Ms, 388 (M⁺); Anal. Calcd for C₂₀H₂₄N₂O₂S₂: C, 61.83; H, 6.23; N, 7.21; S, 16.50%. Found: C, 62.04; H, 6.18; N, 7.13; S, 16.44%.

4. Conclusions

We have developed a straightforward, efficient, and environmentally benign synthetic route to the first reported thiophene bioisosteres of the martinelline alkaloid core. The strategic use of an intramolecular 1,3-dipolar cycloaddition, facilitated by green chemistry principles (ultrasound, heterogeneous catalysis, and CPME), enables the rapid assembly of this complex architecture in excellent yield and with high diastereoselectivity, as confirmed by X-ray crystallographic analysis. Beyond this specific target, the robustness and green credentials of this methodology establish a versatile platform for the synthesis of a diverse array of natural product-inspired heterocycles. This work not only provides access to novel bioactive scaffolds but also underscores the power of sustainable strategies in modern organic synthesis.