Spirocyclic isatin-derivative analogues: Solvation, structural, electronic, topological, reactivity properties, and anti-leukaemic biological evaluation (2023)


The broad range of bioactivity of heterocyclic spiro compounds makes them very interesting and vital for pharmacological applications compared to their cyclic and acyclic analogues. The fascinating feature of the spiro ring system has recently attracted much attention. As pharmacophores, they can interact more efficiently with target proteins thanks to this structure's three-dimensional structure and conformational characteristics [1].

Isatin (1H-indole-2,3-dione), indoline-2,3-dione, is a biologically active heterocyclic moiety. It is a well-known natural substance in Couropita guianensis, Aubl. and plants of the genus Isatis and has also been identified in humans as an adrenaline metabolic product [2]. Two cyclic rings comprise the molecule, one six-membered and the other five-membered, consisting of a nitrogen atom at position 1 and two carbonyl groups at positions 2 and 3. The six-membered ring is aromatic, while the five-membered ring shows anti-aromatic character. These two rings show planar geometry [3]. Erdmann and Laurent were the first to isolate Isatin by obtaining it as a product of the oxidation of Indigo with nitric acid and chromic acid. Isatin derivatives are crucial building blocks for synthesising a wide range of heterocyclic compounds and a starting point for the creation of pharmaceuticals due to their unique property to be used as both electrophiles and nucleophiles [4]. The general methods for the synthesis of isatins are Sandmeyer synthesis, Martinet isatin synthesis, Gassman method and Stolle method. Various heterocyclic frameworks with biological importance, including pyrrolidines, quinolines, indoles, β-lactams, and 2-oxindoles, have been synthesised using isatins as a substrate. Isatin and its derivatives have various biological effects, including analgesic, anti-inflammatory, anti-cancer, anti-bacterial, anti-fungal, anti-diabetic, anti-convulsant, anti-tubercular, anti-HIV, neuroprotective, anti-oxidant, and anti-glycation properties [5].

In the middle of the 20th century, research on producing spirocyclic compounds from isatins began. Due to little to no understanding of the significance of compounds having such frameworks, the investigations did not centre on synthesising spirocyclic frameworks. One of the initial isatin reactions that might have produced a spirocyclic product was its reaction with diazomethane. Several forms of spiroheterocyclic moieties containing 2-oxindoles have been constructed using isatins and their C-3 derivatives. Such compounds are frequently produced directly from isatins through cyclocondensation or cycloaddition reactions with other chemicals. Lately, isatin multicomponent cascade reactions have been used to easily and quickly create spiroheterocyclic frameworks in a single pot. Reactions accomplish Cyclocondensation Synthesis of five- to eight-membered heterocycles. Five- or six-membered spiroazaheterocycles have been reported to be produced through interactions between ammonia, 1,2-diamines, 1,3-diamines and isatins [6].Isatin derivatives that reduce anxiety include 5-hydroxy isatin, isatinic acid, spirobenzodiazepines, and Schiff bases of N-methyl and N-acetyl isatin. Isatin can be used as a chemotherapeutic drug to kill cancer cells and as a preventative measure to prevent free radical-induced cancer. The anticancer activity of novel isatin-based conjugates containing thiazolidine and pyrazoline moieties was examined [4].

In this study, we compare and establish the bioactivity of three structurally related spiro compounds: 4-Methylene-3H-spiro[furan-2,3′-indole]-2′,5(1′H,4H)-dione (MSFID), 1′-(3-Butyn-1-yl)-4-methylene-3H-spiro[furan-2,3′-indole]-2′,5(1′H,4H)-dione (BMSFID) and Methyl 3-(3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl)propanoate (MHIP) using DFT (Density Functional Theory) calculations and docking tests. The isatin-derived spirocyclic analogue MSFID, which contains a Michael acceptor, has been studied in vitro and in vivo and has shown to inhibit tumour necrosis factor-alpha (TNFα)-induced IκB kinase β (IKKβ)-mediated nuclear factor kappa B (NF-κB) activation, which is essential for innate and adaptive immune responses, inflammation, cell growth, and apoptosis, and, in addition to this study, all three title molecules’ synthesis, experimental data and structure–activity-relationships are reported by Rana and co-workers. Growth inhibitory activity is only slightly affected by BMSFID (methylated at the nitrogen atom on oxindole), and MHIP, the acyclic analogue, shows about two folds less activity when compared with MSFID [7]. A thorough literature investigation reveals that DFT analyses on these molecules have not yet been carried out. The theoretical studies in this work further support the effectiveness of these compounds in fighting cancer.

The structural and electronic characteristics are predicted via DFT investigations. To get knowledge about the reactivity of the molecules as well as their electron density and interactions, wavefunction analyses like ELF (Electron Localization Function), LOL (Localized Orbital Locator), RDG (Reduced Density Gradient) and charge transfer studies are also carried out [8], [9], [10]. Visualising the electrophilic and nucleophilic sites within the molecules is made possible by MEP (Molecular Electrostatic Potential) analysis. NBO (Natural Bond Orbital) and UV studies are also done. NLO (Non-Linear Optics) is used to determine if the molecular properties may be used for NLO applications, which are widely employed in fields like industry and medicine. The reference material used in this comparison is urea [11], [12]. Since urea has many medicinal chemistry parameters, it has been considered the standard substance for NLO studies. The pharmacological evaluation of the molecules is done to obtain ADME profiles, which describe the different chemistry parameters of the molecules, and docking is conducted to predict how the molecules interact with select target proteins. Researchers have performed similar studies on organic molecules to gain a better understanding of how these molecules may act [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23]. Important drug parameters like lipophilicity and BBB (blood–brain barrier) permeability may now be predicted using deep learning models with great accuracy [24], [25].

All Gaussian calculations are based on DFT, which provides high accuracy for large organic molecules at a low computational cost compared with other methods like Hartree-Fock. In this case, energy is considered a function of energy density. By excluding the number of electrons from the equation, it is not necessary to consider this quantity, which can be a large number for systems containing more than two atoms, making the Schrödinger equation impossible to solve. Therefore, when using DFT, the energy density can be calculated independently of the total number of electrons within the system under study, which is much simpler than traditional Hartree-Fock calculations [26], [27].

This study uses the highest basis set available for the B3LYP functional [28], [29], [30], [31], [32], the 6-311G++(d,p) basis set, for Gaussian DFT and TD-DFT calculations. With higher basis sets, calculation errors are less likely to arise from truncation [33]. Hence much accuracy is achieved in the calculations at a lower cost computationally.

The IEFPCM solvation method is used to study the behaviour of organic molecules with solvent media. This is interesting in biological studies as biochemical reactions and interactions occur in solution. Water is paramount in this regard, as it is the solvent in living cells. The IEFPCM model is a popular continuum model used for solvation studies [34]. Solvents that are polar and protic can donate the hydrogens from NSpirocyclic isatin-derivative analogues: Solvation, structural, electronic, topological, reactivity properties, and anti-leukaemic biological evaluation (1)H and OSpirocyclic isatin-derivative analogues: Solvation, structural, electronic, topological, reactivity properties, and anti-leukaemic biological evaluation (2)H bonds, thus increasing hydrogen bonds in the organic molecules and causing a shift in their properties. In order of polarity, the solvents belonging to this category in this work are ethanol, methanol and water. DMSO, a polar aprotic solvent, cannot donate protons, yet because of van der Waals interactions with the organic molecules, it can cause solvent effects of significance as well [35].

The molecular structures of the title compounds are first optimised by geometry optimisation. The stable systems obtained are used to compute the frontier orbitals and the global reactivity parameters. MEP studies determine the regions of chemical reactivity within the compounds. NLO analysis is also performed. The UV studies employ the TD-DFT/M06-2X [36], [37], [38], [39] method. Multiwfn software is used to obtain the output for the topological analysis. The Lamarckian Genetic Algorithm, one of the most successful algorithms in determining the binding free energies, is used in the docking procedure [40].

Section snippets

Computational details

The DFT simulation uses Gaussian 09W and GaussView06 [41], [42] software, allowing output visualisation. The graphical portrayal of geometry-optimized structures and the acquisition of related data are done using Chemcraft 1.8 [43]. For the most precise basis set (the common 6-311G++(d,p) basis set), the B3LYP hybrid functional is used [28], [29], [30], [31], [32]. TD-DFT/M06-2X [36], [37], [38], [39] method is employed for the UV studies by requesting the default number of excited states in

Geometrical optimization

Optimisation of the molecular compounds was done in vacuum and solvent media. BMSFID analogue was observed to have the most stable structure in both the gas phase and solvents, showing a tremendous negative total energy of −896.133 Hartree. The other two compounds, MSFID and MHIP, have energy from −740 to −860 Hartree. As the structures of all compounds are solvated, they become more stable in solution, with the stabilisation increasing with solvent polarity. All title compounds show maximum


Pauli repulsion in atomic orbitals is shown by the electron localisation function (ELF) study [49]. The ELF maps of the title compounds in gas and solvent phases are displayed in Fig. 2. Pauli’s repulsion is most substantial in the red areas, as seen for the aromatic ring hydrogens. Due to their tiny size, the 1s atomic orbitals of hydrogen exhibit high Pauli repulsion when interacting with nearby orbitals. The blue patches depict weak Pauli repulsion in the bigger sp3-hybridized orbitals of

Frontier molecular orbitals (FMO) analysis

The FMO analysis is carried out to determine the molecules' level of reactivity [50]. This study evaluates several parameters, which are listed in Table 4. The three compounds' FMO 3D plots in the gas phase are shown in Fig. 6.

The global as well as local reactivity parameters are derived from the expressions [50], [54], [55]:η=12EHOMO-ELUMO;global hardnessζ=1η;global softnessμ=12EHOMO+ELUMO;chemical potentialω=μ22η;global electrophilicity indexIP=-EHOMO;ionisation potentialEA=-ELUMO;electron

MEP analysis

Electrophilic and nucleophilic active regions within the molecules are depicted in the colour-coded MEP maps in Fig. 8 [55]. According to these maps, electrophilicity increases from left to right as Blue<Green<Yellow<Orange<Red [55], [57]. Those regions that are the most nucleophilic are coloured blue, and those that are the most electrophilic are coloured red. As expected from Fig. 7, molecular oxygens are electrophilic and therefore are shown in the red region. Similarly, the

NBO analysis

NBO analysis by DFT technique predicts the occupation and stabilisation energies of molecular orbitals, and it provides an insight into those orbitals which contribute most to the stabilisation of the molecule [58].

E(2) (stabilisation energy) is calculated in this study by the following equation:E(2)=ΔEij=qiFi,j2εj-εi

where (Fi, j) represents the off-diagonal NBO Fock matrix element, εj and εi are the diagonal elements, and qi is the occupancy of the donor orbital. Higher E(2) values mean

Non-Linear optical (NLO) properties

To assess how high-intensity light interacts with appropriate materials for diverse uses in industry, medicine, etc., NLO qualities are examined. Pi-orbital polarisation and the interaction of the molecule's donor and acceptor sites cause NLO behaviour [59]. The B3LYP technique and standard basis set are used to compute the NLO parameters, which are the dipole moment (μ), polarizability (α), and first-order hyperpolarizability (β), theoretically in the gas phase. The outcomes are displayed in

ADME profile

To confirm the drug-likeness of the title compounds, ADME profiling evaluates properties such as water solubility, lipophilicity, and other vital parameters. In addition, the different compounds should adhere to the critical Lipinski rule of five [60]. ADME is an abbreviation for Absorption, Distribution, Metabolism and Excretion. The ADME profile of the compounds is evaluated here using SwissADME online tool [45], and the results are displayed in Table 8. All three compounds have ideal


This work investigates the solvation effect and structural, electronic and biological properties of the isatin-derived spirocyclic analogues with α-methylene-γ-butyrolactone cores. Based on this work's studies, BMSFID has emerged as the most stable molecule in all media, vacuum, and different solvents. Geometry optimisation and the FMO analysis reveal that the BMSFID analogue is also the most reactive. ELF, LOL, and RDG studies reveal the non-covalent interactions within the molecule. Charge

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

© 2023 Elsevier B.V. All rights reserved.

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