6,8-Dibromo-11H-indeno[1,2-b]quinolin-11-one

Abstract

We report the synthesis of the new compound 6,8-dibromo-11H-indeno[1,2-b]quinolin-11-one, which presents an important type of nitrogen-containing heterocycles and is a useful intermediate product in organic synthesis. The structure of the compound was confirmed by the single crystal X-ray diffraction. Molecular docking analysis revealed that 6,8-dibromo-11H-indeno[1,2-b]quinolin-11-one may effectively intercalate with DNA. The synthesized indenoquinoline derivative thus represents a promising lead compound for developing targeted anticancer and anti-inflammatory drugs.

1. Introduction

Heterocycles containing the quinoline ring constitute a wide variety of biologically active compounds. For example, Asao and colleagues reported the antitumor activity of some derivatives with the indeno[1,2-c]quinolin-11-one scaffold [1]. Compound TAS-103 containing the indeno[2,1-c]quinoline moiety (Scheme 1) has been proved to be a novel Top I and Top II targeting agent that stabilizes cleavable complexes of Top-DNA at the cellular level [2,3,4]. A number of furo[2,3-b]quinoline derivatives, such as CIL-102, have also been synthesized and demonstrated to possess significant anticancer activity [5,6,7,8,9]. The bis(indeno[1,2-b]quinoline-6-carboxamides), e.g., Compound A (Scheme 1), are an interesting new class of putative topo I inhibitors, some exhibiting very high cytotoxicity in cell culture (Murine P388 leukemia, Murine Lewis lung carcinoma, wild-type human Jurkat leukemia, amsacrine-resistant Jurkat, doxorubicin-resistant Jurkat), and activity comparable to irinotecan against sub-cutaneous colon 38 tumors in vivo [10]. Some indenoquinoline derivatives, such as Compound B, showed cytotoxicities comparable to those of camptothecin against MCF-7 and HeLa cells [11].

Indenoquinolines are analogs of the indenoquinoxaline-based c-Jun N-terminal kinase (JNK) inhibitors [12,13] with 11H-Indeno[1,2-b]quinoxalin-11-one oxime (IQ-1) parent scaffold. Their structural similarity suggests that they share a common or closely related pharmacophore. Hence, indenoquinolines could represent a new class of JNK inhibitors with distinctive pharmacological properties.

Indenoquinolines can be prepared by reducing 2-(2-nitrobenzylidene)-1,3-indanediones with sodium dithionite or tin chloride (Scheme 2, route a). However, it is necessary to preliminarily obtain the benzylidene derivative by the condensation of 1,3-indanedione with an aromatic aldehyde [14]. The conversion of methyl 1-arylamino-3-oxoindan-2-dithiocarboxylates under reflux in diphenyl ether gave the corresponding sulfur-containing indenoquinolines, which were subsequently subjected to desulfurization with Raney nickel and gave indenoquinoline derivatives (Scheme 2, route e) [15]. Other synthetic strategies for indenoquinoline involve Pfitzinger synthesis from an isatin and 1-indanone with further oxidation by Na₂Cr₂O₇ in sulfuric acid (Scheme 2, route b) [16], palladium-catalyzed intramolecular arylation (Scheme 2, route c) [17], Pd-mediated simultaneous C–H (aldehyde) and C–X bond activation (Scheme 2, route d) [18], iron/AcOH promoted intramolecular cyclization (Scheme 2, route f) [19], TBHP promoted intramolecular carbonylation (Scheme 2, route g) [20].

Most of these reported preparations include multiple steps and utilize precursors with limited availability. In this paper, we report the previously unknown indenoquinoline derivative 6,8-dibromo-11H-indeno[1,2-b]quinolin-11-one, which was synthesized using a catalyst-free methodology and can be considered as a promising biologically active compound.

2. Results and Discussion

2.1. Chemistry

For the preparation of the indenoquinoline derivative, we used the Friedländer reaction, which occurs between 2-aminobenzaldehyde and ketone without a catalyst. The Friedländer annulation is still the most simple and straightforward method for the synthesis of poly-substituted quinolines. Previously, this method was studied by Chinese scientists for obtaining various compounds with quinoline moiety [21]. The authors used 2-aminobenzaldehyde and 1,3-indandione for the synthesis of 11H-indeno[1,2-b]quinolin-11-one in a high yield. In 2019, a patent was issued describing the use of deionized water as a solvent for obtaining this ketone in 92% yield [22]. We decided to expand the library of known indenoquinolines by Friedländer synthesis of the corresponding dibromo derivative.

Our attempt to carry out the condensation between 2-amino-3,5-dibromobenzaldehyde (1 equiv., Compound 1) and 1,3-indandione (1 equiv., Compound 2) in water at 70 °C, following protocols from [21,22], did not lead to a complete conversion of the starting materials, presumably due to a low solubility of the bromine-substituted precursor. In this regard, we applied another system that had not been previously used to obtain indenoquinolines. A mixture of compounds 1 (1 equiv.) and 2 (1 equiv.) was refluxed in acetonitrile with 1,3-dicyclohexylcarbodiimide (DCC, 1 equiv.), which played the role of a water-removing agent (Scheme 3). Under these conditions, the reaction proceeded to complete conversion, affording 6,8-dibromo-11H-indeno[1,2-b]quinolin-11-one (Compound 3) in 40% crude yield. No by-products were detected by TLC. The moderate yield reflects the compound’s partial solubility in the reaction medium and purification losses.

The structure was confirmed by the NMR data (Figures S1 and S2), IR spectroscopy (Figure S3), LC/MS analysis (Figure S4) and single crystal X-ray diffraction. The main characteristics of the title Compound 3: bright orange crystals, m.p. 276–279 °C, soluble in acetone and chloroform.

2.2. X-Ray Crystal Structure

Compound 3 crystallizes in a monoclinic crystal system, space group P2₁/n. The asymmetric unit consists of one molecule of 3 (Figure 1a). The pairs of molecules are linked by two bifurcated C–H···O contacts with the internuclear distances of 2.527 Å and 2.602 Å (Figure 1b). These pairs are further joined by C–H···π contacts (internuclear H···C_Ar distance 2.752 Å) into zig-zag supramolecular chains, oriented along the (a + c) crystallographic direction (Figure 1c). Along the crystallographic axis b, the indeno[1,2-b]quinolin-11-one cycles are involved in π-π stacking interactions, with the distance between the planes of the cycles being 3.447 Å and centroid-to-centroid distance 3.952 Å (Figure 1b).

2.3. Molecular Docking Study of DNA Intercalation

In order to study the potential of planar molecule 3 to act as a DNA intercalator, we performed molecular docking of Compound 3 into the B-DNA structure (PDB: 151D) [23]. The binding region used for the intercalation modeling corresponded to the position of the known anticancer drug doxorubicin inserted between the guanine (G) and cytosine (C) base pair in the 151D structure. Docking was performed using the ROSIE server and resulted in the position of Compound 3 shown in Figure 2. In the found pose, molecule 3 is oriented similarly to the planar fragment of doxorubicin and participates in π-π stacking interactions with the neighboring G and C bases.

The obtained docking pose is characterized by an Interface Score value of −10.89 kcal/mol, which indicates the possibility of efficient intercalation of Compound 3 into DNA.

3. Materials and Methods

3.1. General Information and Compound 3 Synthesis

LC/MS analysis was performed on an Agilent Infinity chromatograph with an AccurateMass QTOF 6530 mass detector. Chromatographic conditions: column Zorbax EclipsePlusC18 1.8 μm, 2.1 × 50 mm; eluent H₂O: ACN (85%); flow 0.2 mL/min. Ionization source: ESI in positive mode. The elemental analysis was made using a Carlo Erba analyzer (Thermo Fisher Scientific, Waltham, MA, USA). The IR spectrum was recorded on an Agilent Cary 630 FTIR spectrometer. The ¹H and ¹³C NMR spectra were recorded on a Bruker AVANCE III HD instrument (operating frequency ¹H—400 MHz; ¹³C—100 MHz). The melting point of the obtained compound was measured using a Melting Point Apparatus SMP30, heating rate 2.5 °C/min. The reaction was monitored by a thin layer chromatography (TLC) on Silufol UV-254 and Merck plates, silica gel 60, F254.

6,8-Dibromo-11H-indeno[1,2-b]quinolin-11-one (3). To a solution of Compound 1 (1 mmol) in acetonitrile (10 mL), Compound 2 (1 mmol) was added on permanent stirring. Then, DCC (1 mmol) was added, and the mixture was refluxed for 1.5 h. The reaction was monitored by TLC (eluent: chloroform). After cooling, the precipitate was filtered out and washed with ethanol. Purification was carried out by column chromatography on silica gel (eluent: chloroform). The title Compound 3 was obtained as orange crystals (yield 40%); M.p. 276–279 °C (from ethanol).

¹H NMR (400 MHz, CDCl₃), δ, ppm: 8.24 (s, 1H, H-10), 8.19 (d, J = 8 Hz, 1H, H-14), 8.18 (s, 1H, H-6), 7.99 (d, J = 2 Hz, 1H, H-2), 7.85 (d, J = 7.5 Hz, 1H, H-17), 7.73 (t, J = 6 Hz, 1H, H-15), 7.57 (t, J = 6 Hz, 1H, H-16) (atom numbering is shown in Figure 3). ¹³C NMR (100 MHz, CDCl₃), δ, ppm: 190.3, 163.1, 146.7, 143.6, 138.4, 137.6, 136.1, 132.4, 132.2, 131.6, 130.0, 128.5, 126.5, 124.5, 122.8, 120.6. Found, %: C 49.23, H 1.72, N 3.70, C₁₆H₇Br₂NO, Calculated, %: C 49.40, H 1.81, N 3.60. IR spectrum: 676 (C-Br); 1483 (C=N); 1625 (arom.); 1711 (C=O). LC/MS (ESI+), m/z: 387.8971 experimental ([C₁₆H₇Br₂NO + H]⁺ = 387.8967 theor.); exit time 140–170 s. The ratio of isotopic peaks corresponds to the theoretical m/z: 387.8971 (50%), 388.9000 (<10%), 389.8947 (100%), 391.8926 (50%).

The ¹H NMR, ¹³C NMR, IR, and MS spectra are shown in Figures S1–S4.

3.2. X-Ray Crystal Structure Determination

The X-ray diffraction data for single crystals of Compound 3 were collected at 291(2) K on an automated Agilent Xcalibur four-circle diffractometer equipped with an area AtlasS2 detector. Graphite-monochromated MoKα radiation (λ = 0.71073 Å) was used. Absorption corrections were applied with the use of the SADABS program [24]. The crystal structures were solved and refined by means of the SHELXT [25] and SHELXL [26] programs. Atomic thermal displacement parameters for non-hydrogen atoms were refined anisotropically. The hydrogen atoms were placed geometrically and refined using the riding model. The crystallographic data and details of the structure refinement are summarized in

Table 1. Crystallographic data of Compound 3.

Parameter	Value
Empirical formula	C16H7NOBr2
Formula weight	389.05
Temperature, K	291 (2)
Crystal system	monoclinic
Space group	P21/n
a, Å	15.5188 (8)
b, Å	3.9524 (2)
c, Å	21.8263 (10)
β, °	93.262 (4)
Volume, Å3	1336.58 (11)
Z	4
ρcalc, g/cm3	1.933
μ, mm−1	6.057
F(000)	752.0
Crystal size, mm3	0.25 × 0.10 × 0.03
2Θ range for data collection, °	5.258 to 58.558
Index ranges	−19 ≤ h ≤ 12, −5 ≤ k ≤ 5, −28 ≤ l ≤ 29
Reflections collected	6164
Independent reflections	2963 [Rint = 0.0537, Rsigma = 0.0561]
Data/Restraints/Parameters	2963/0/181
Goodness-of-fit on F2	1.077
Final R indexes [I ≥ 2σ (I)]	R1 = 0.0475, wR2 = 0.1146
Final R indexes [all data]	R1 = 0.0640, wR2 = 0.1359
Largest diff. peak/hole, e·Å−3	0.61/−0.78

.

3.3. Molecular Docking

Docking of Compound 3 into B-DNA (structure 151D from the Protein Data Bank) was performed using the ROSIE server [27]. The docking area was chosen around the geometric center of the doxorubicin molecule co-crystallized in the 151D structure. The number of intermediately generated docking poses was set to 1000. Other options were used as defaults within the ROSIE ligand docking protocol. After completion of the computations, a PDB file containing the best docking pose of Compound 3 was downloaded from the server and imported into the Molegro Virtual Docker 6.0 (MVD) program for visualization and analysis using the built-in “Pose Organizer” tool of MVD.

4. Conclusions

In this work, we present the synthesis of the previously unknown Compound 3 (6,8-dibromo-11H-indeno[1,2-b]quinolin-11-one). For the first time, a catalyst-free system, MeCN/DCC, was tested for obtaining an indenoquinoline derivative. The compound structure was confirmed by NMR, IR, X-ray diffraction, LC/MS, and elemental analyses. Compound 3 has structural similarity to IQ-1 and is promising as a JNK inhibitor like other indenoquinoxaline analogs [13]. The possibility of intercalation into DNA similarly to doxorubicin was shown by the molecular docking computations. The title compound 3 demonstrates significant potential as a lead structure for biological activity studies.