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Research Article
Design, synthesis and biological evaluation of novel 2-hydroxy-1 H-indene-1,3(2 H)-dione derivatives as FGFR1 inhibitors
expand article infoMohammed M. Al-Mahadeen‡, Areej M. Jaber§, Belal O. Al-Najjar§
‡ The University of Jordan, Amman, Jordan
§ Al-Ahliyya Amman University, Amman, Jordan

Corresponding author: Mohammed M. Al-Mahadeen ( malmahadeen@yahoo.com )

Corresponding author: Areej M. Jaber ( a.jaber@ammanu.edu.jo )

Academic editor: Plamen Peikov
© 2024 Mohammed M. Al-Mahadeen, Areej M. Jaber, Belal O. Al-Najjar.
This is an open access article distributed under the terms of the CC0 Public Domain Dedication.
Citation: Al-Mahadeen MM, Jaber AM, Al-Najjar BO (2024) Design, synthesis and biological evaluation of novel 2-hydroxy-1 H-indene-1,3(2 H)-dione derivatives as FGFR1 inhibitors. Pharmacia 71: 1-9. https://doi.org/10.3897/pharmacia.71.e122127
Open Access

Abstract

Fibroblast growth-factor receptor (FGFR) is a potential target for cancer therapy. We synthesised a novel series of FGFR1 inhibitors bearing quinoline, quinoxalin and isoquinoline using a synthetic strategy employing a one pot reaction, yielding 2-hydroxy-1H-indene-1,3(2H)-dione. Structural elucidation via IR, NMR and HRMS analyses is complemented by a proposed mechanistic pathway. All newly-synthesised compounds were evaluated in vitro for their inhibitory activities against FGFR-1. The most potent derivatives were 9a, 9b, 9c and 7b with IC50 = 5.7, 3.3, 4.1 and 3.1 μM, respectively, supported by molecular docking studies which probed the binding interactions of these compounds within the active site of the kinase.

Keywords

anticancer, Imidazo, Indene, FGFR1 inhibitor, molecular docking

To the memory of the late Prof. Mustafa M. El-Abadelah

Introduction

Aza-arenes (e.g. pyridine, quinoline, isoquinoline) are hyperaromatic aza-arene systems in which the bridgehead N-4 contributes to the aromaticity with its lone pair. Therefore, this nitrogen atom is not nucleophilic and the attack occurs at N-2 position. This parent compound is known to undergo electrophilic substitution (SE–Ar) with various electrophiles at C-1, but also at C-3 or both, depending on the reaction conditions used (Katritzky et al. 2008). Consequently, acetylation of imidazo N-heterocycles commonly occurs at either the C-1 (Bower and Ramage 1955; Jaber et al. 2020) or C-3 (Hlasta and Silbernagel 1998) position, while nitrosation (followed by re-arrangement) typically targets the C-1 position (Paudler and Kuder 1967). Mono-formylation predominantly takes place at C-1 (70%) with a lesser extent at C-3 (30%) (Fuentes and Paudler 1975). Conversely, lithiation and related methods for generating carbanions favour C-3 (Paudler et al. 1972; Fuentes and Paudler 1975). When C-1 is blocked, electrophilic substitution primarily occurs at C-3 (Anderson and Watt 1995; Katritzky et al. 2008). Recently, El-Abadelah et al. investigated the reaction between 3-(substituted) imidazo[1,5-a]pyridines (1) and ninhydrin (2). This reaction involves the nucleophilic addition of the central carbonyl carbon of ninhydrin to C-1 of imidazo[1,5-a]pyridines, yielding the respective products 3a–g (Scheme 1) (Sammor et al. 2018; El-Abadelah et al. 2020; Al-Mahadeen et al. 2022; Jaber et al. 2023b).

Scheme 1. 

Synthesis of 2-hydroxy-2-(imidazo[1,5-a]pyridinyl)indene-1,3(2H)-diones.

Depending on that, we deemed it valuable to examine the reaction between ninhydrin and imidazo N-heterocycles (such as quinoline, isoquinoline and quinoxaline) under neutral conditions. Additionally, we explored potential novel biological activities stemming from these reactions (,Shehadi et al. 2020; Jaber et al. 2022; Jaber et al. 2023a). Herein, we present our findings on both reactions, as depicted in Scheme 2 below, with a specific emphasis on their potential as inhibitors of fibroblast growth factor receptors (FGFR1).

Scheme 2. 

Synthesis of compounds 7–9.

Scheme 3. 

Synthesis of compounds 4–6.

Materials and methods

Experimental part

Quinoline-2-carbaldehyde, isoquinoline-1-carbaldehyde, quinoxaline-2-carbaldehyde, dimethyl acetylenedicarboxylate (DMAD), ninhydrin, (±) Phenylglycine, L-phenylalanine, L-alanine and dichloromethane were procured from Acros. FTIR spectra were recorded using a Thermo-Nicolet Nexus 670 FTIR instrument. 1H-NMR and 13C-NMR spectra were acquired on a Bruker Avance III-500 MHz spectrometer with TMS serving as the internal standard. Chemical shifts were expressed as δ values in ppm. Carbon atom multiplicities were determined from DEPT experiments. High-resolution mass spectra (HRMS) were obtained using the electrospray ion trap (ESI) technique with collision-induced dissociation on a Bruker APEX-IV (7 Tesla) instrument. Solvents utilised in the study were sourced from Acros or Aldrich.

Chemistry

General procedure for the preparation of compounds (4–6)

These compounds were prepared from the reaction of appropriate amino acid with the appropriate aza-arene carboxaldehyde (in the presence of iodine I2, potassium bicarbonate KHCO3 and powder molecular sieves 4 Å) according to a reported procedure (Wang et al. 2012; Jaber et al. 2020; Al-Mahadeen et al. 2022).

General procedure for synthesis compounds (7–9)

A solution containing 5 mmol of imidazo compounds 4–6 in 30 ml of anhydrous dichloromethane was added to a stirred solution of ninhydrin 2 (5 mmol) in 25 ml of dichloromethane at room temperature. The resulting mixture was stirred for an additional 3–4 hours at room temperature. Subsequently, the solvent was removed under vacuum, and the remaining crude product was purified by chromatographic separation on silica gel TLC plates, with elution achieved using a mixture of n-hexane and ethyl acetate (3:1, v/v).

Results and discussion

Chemistry

In this study, the direct interaction of ninhydrin 2 with the imidazo derivatives 4–6 in dichloromethane at room temperature yielded the expected adducts 7–9 in high yields Scheme 2. The newly-synthesised compounds underwent identification and characterisation using IR, NMR and HRMS spectral data and their structures were validated through single-crystal X-ray structure determination. The collected data consistently supported the proposed structures. Notably, mass spectra exhibited accurate molecular ion peaks and HRMS spectral data aligned closely with calculated values. DEPT and 2D (COSY, HMQC and HMBC) experiments aided in assigning signals to different carbons and their attached and neighbouring hydrogens. We confirmed the structures by single crystal X ray structure determination for 9b (Fig. 1), representing the series.

Figure 1. 

ORTEP view of the molecular structure and atom numbering scheme of 9b.

X-ray structure determination of 9b

To confirm the structure of 9b (Scheme 2), X-ray crystal structure determination was conducted. A summary of the data collection and refinement parameters is provided in Table 1. The molecular structure of 9b, as derived from crystallographic data, is depicted in Fig. 1. Notably, the two aromatic systems exhibit a nearly perpendicular orientation to each other, with an angle of 81° between their respective planes. This perpendicular alignment is stabilised by attractive forces between N1 and the carbonyl carbon (C22), with a distance of 2.744 Å between the two atoms, approximately 0.5 Å less than the sum of van der Waal’s radii. Such interactions between electron-deficient carbon atoms of carbonyl groups and electronegative atoms have been frequently documented in the literature (Braga et al. 2009).

Table 1.
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Crystal data and structure refinement for 9b.

Empirical formula C28H22N2O4S
Formula weight, g mol-1 482.53
Temperature, K 100
Crystal system monoclinic
Space group P21/n
a, Å 16.525(6)
b, Å 8.346(3)
c, Å 17.532(7)
α/° 90
β/° 103.530(12)
γ/° 90
Volume, Å3 2350.9(15)
Z 4
Density (calcd.), g cm-3 1.363
Absorption coefficient μ/mm1 0.176
F (000), e 1008.0
2Θ range for data collection, deg 3.87 to 61.194
Index ranges hkl -21 ≤ h ≤ 23, -11 ≤ k ≤ 11, -25 ≤ l ≤ 24
Reflections collected 83166
Independent reflections 7175 [Rint = 0.0884, Rsigma = 0.0421]
Absorption correction Semi-empirical from equivalents
Refinement method Full-matrix least-squares on F2
Data/ restraints/ parameters 7175/ 0/ 320
Final R indexes [I ≥ 2σ (I)] R1 = 0.0547, wR2 = 0.1391
Final R indexes [all data] R1 = 0.0775, wR2 = 0.1681
Largest diff. peak/hole, e Å-3 0.29/-0.42

aR1 = Σ||Fo| – |Fc||/Σ|Fo|; bwR2 = [Σw(Fo2 −Fc2) 2/Σw (Fo2) 2] 1/2.

Molecular docking

Molecular docking simulations were performed to shed light on the molecular processes that contribute to the anticancer effects of the created compounds on the FGFR1 protein. To ensure the accuracy of the docking process, the co-crystal structure of erdafitinib was re-docked Fig. 2, resulting in an RMSD value of 0.76 Å, as shown in Fig. 3. The RMSD value, which is less than the 2 Å limit, verifies the dependability of the docking protocol for future analyses (Hevener et al. 2009).

Figure 2. 

Solid ribbon representation of FGFR1 (PDB ID: 5EW8) with co-crystal (grey) and re-docked (orange) erdafitinib. Generated by Biovia Discovery Studio visualizer®.

Figure 3. 

Stick representation of a. Erdafitinib; b. 7b; c. 9a; d. 9b; e. 9c in grey colour, docked within FGFR1 (PDB ID: 5EW8) binding site (green). Generated by Biovia Discovery Studio visualizer®.

The molecular docking simulation results for the compounds 7b, 9a, 9b and 9c against FGFR1 are presented in Table 2. The free energy of binding (in kcal/mol) indicates the strength of the interaction between the compound and the target protein, with lower values indicating stronger interactions.

Table 2.
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Lowest binding Energy in kcal/mol of the Docked Compounds 7b, 9a, 9b and 9c against FGFR1 binding site.

# Compound Lowest Binding Energy (kcal/mol) Interacting Residues
Hydrogen Bond Hydrophobic Pi-Anion
1. 7b -8.97 Asp641 Leu484, Val492, Ala512, Lys514, Val561, Ala564, Leu630 NI
2. 9a -8.02 Asp641 Leu484, Val492, Ala512, Lys514, Ile545 Val561, Ala564, Leu630 Glu531
3. 9b -9.23 Lys514, Asp641 Leu484, Val492, Lys514, Val561, Leu630 NI
4. 9c -9.18 Asp641 Leu484, Val492, Ala512, Lys514, Val561, Arg627, Leu630 NI
5. Erdafitinib (Reference) -11.16 Ala564, Asp641 Leu484, Val492, Ala512, Lys514, Ile545, Val561, Leu630, Ala640 Asp641

NI = No Interaction.

Compound 7b exhibits a free energy of binding of -8.97 kcal/mol, with Asp641 performing hydrogen bond interaction and several residues (Leu484, Val492, Ala512, Lys514, Val561, Ala564, Leu630) performing hydrophobic interactions. However, no Pi-Anion interactions were observed. Compound 9a shows a slightly weaker binding energy of -8.02 kcal/mol. It interacts with Asp641 through hydrogen bonding and with several residues (Leu484, Val492, Ala512, Lys514, Ile545, Val561, Ala564, Leu630) through hydrophobic interactions. Notably, it also exhibits Pi-Anion interactions with Glu531. Compounds 9b and 9c exhibit stronger binding energies of -9.23 kcal/mol and -9.18 kcal/mol, respectively. Compound 9b forms hydrogen bonds with Lys514 and Asp641 and hydrophobic interactions with Leu484, Val492, Lys514, Val561 and Leu630. Compound 9c forms a hydrogen bond with Asp641 and hydrophobic interactions with Leu484, Val492, Ala512, Lys514, Val561, Arg627 and Leu630. Neither compound shows Pi-Anion interactions. For comparison, the reference compound Erdafitinib exhibits a binding energy of 11.16 kcal/mol, indicating a stronger interaction with FGFR1. It forms hydrogen bonds with Ala564 and Asp641, hydrophobic interactions with Leu484, Val492, Ala512, Lys514, Ile545, Val561, Leu630 and Ala640 and a Pi-Anion interaction with Asp641.

An interesting trend emerged, suggesting a moderate correlation between the predicted binding affinity and the in vitro inhibitory activity. Compound 9b, which exhibited the most favourable docking score (Lowest Binding Energy = -9.23 kcal/mol) with additional hydrogen bond interaction with Lys514, Asp641, also displayed the most potent inhibitory effect (IC50 = 3.3 μM).

Similarly, compound 7b, with the second-highest binding affinity (-8.97 kcal/mol) and interaction with Asp641, demonstrated a notable inhibitory effect (IC50 = 3.1 μM).

However, a perfect correlation was not observed. Compounds 9c and 9a displayed comparable binding energies (-9.18 and -8.02 kcal/mol, respectively) and interacted with Asp641. However, their in-vitro potencies differed, with 9c exhibiting a lower IC50 (4.1 μM) compared to 9a (5.7 μM). This discrepancy suggests that other factors beyond the predicted binding energy and the primary interacting residues might also influence the inhibitory activity of these compounds.

Evaluation of biological activities

We assessed the cytotoxic activities of the prepared compounds against fibroblast growth factor receptors (FGFR1) inhibitors. Notably, Table 3 shows the inhibitory profiles of 7a-c, 8a-c and 9a-c. Clearly, 7b, 9a, 9b and 9c have superior inhibitory percentages compared to other compounds prompting us to pursue their IC50 values. Fig. 4 shows the resulting dose/response curves and IC50 values.

Table 3.
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Percent inhibition values of FGFR1 at 10 µM concentration of the prepared compounds. Staurosporine was included as a control.

Compound % Inhibition at 10 μMa IC50 (μM)
7a 8 NDb
7b 40 3.1
7c 12 NDb
8a 6 NDb
8b 8 NDb
8c 7 NDb
9a 43 5.7
9b 32 3.3
9c 39 4.1
Staurosporinec 12.12 nM

aAverage of duplicate measurements ± standard deviation. bND: Not determined. cStandard inhibitor.
Figure 4. 

Dose-response curves of compounds 7b, 9a, 9b and 9c FGFR1 inhibitor. A. Dose-response curve of 7b with IC50 = 3.1 μM; B. Dose-response curve of 9a with IC50 = 5.7 μM; C. Dose-response curve of 9b with IC50 = 3.3 μM; D. Dose-response curve of 9c with IC50 = 4.1 μM.

Conclusions

This study explores a novel range of compounds featuring quinoline, quinoxalin and isoquinoline as potential inhibitors of FGFR1. These compounds were synthesised via the direct interaction of ninhydrin with imidazo derivatives. In vitro testing revealed that, while all compounds exhibited weak inhibitory activity against FGFR1, compounds 9a, 9b, 9c and 7b demonstrated IC50 values of 5.7, 3.3, 4.1 and 3.1 μM, respectively. Molecular docking simulations on the FGFR1 protein binding site suggested that the anticancer effects may arise from enzyme inhibition. Additionally, in silico studies indicated favourable pharmacokinetic properties, offering promise for the development of novel cancer therapeutics with enhanced efficacy and specificity in the future.

Acknowledgements

The authors would like to pay tribute to the late Professor Mustafa M. El-Abadelah, who was always willing to offer guidance and support throughout his professional and scientific career.

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Supplementary material

Supplementary material 1 

Design, synthesis and biological evaluation of novel 2-hydroxy-1H-indene-1,3(2H)-dione derivatives as FGFR1 inhibitors

Mohammed M. Al-Mahadeen, Areej M. Jaber, Belal O. Al-Najjar

Data type: pdf

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
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