Targeting human 5- Lipoxygenase: An In silico study on the antipsoriatic potential of Melia dubia Phytocompounds

Psoriasis is a chronic immune-mediated inflammatory skin disorder in which the immune system becomes overactive, causing skin cells to multiply too quickly. It affects the global population and is influenced by genetic, immunological, and environmental factors. In addition to cutaneous manifestations, psoriasis is associated with systemic comorbidities, including cardiovascular disorders, mental health problems, cancer, diabetes, and metabolic syndrome. Common symptoms of psoriasis include patches of thick, red skin with silvery-white scales, poor sleep quality, and dry, cracked skin that itches or bleeds. Contemporary research emphasizes the therapeutic potential of medicinal plants in treatment of psoriasis due to their anti-inflammatory and immunomodulatory properties (Rajashekar et al., 2016). Medicinal plants represent a rich repository of bioactive compounds with diverse pharmacological activities. Melia dubia is considered one of the largest fast-growing trees belonging to the family Meliaceae. The common name of Melia dubia is Malabar neem. The fruit of Melia dubia is small, yellow, fleshy, and dorsally compressed. It has important industrial applications and is increasingly used as a source of energy. Apart from its industrial applications, Melia dubia fruit is widely used for various medicinal applications because of its reported anticancer, anti-inflammatory, and antimicrobial activities (Halliwell, 2007). The inflammatory cascade of psoriasis is regulated by a complex network of enzymes and signalling molecules, among which Human 5-Lipoxygenase (PDB ID: 3V99) plays a pivotal role in leukotriene biosynthesis and mediator production. Targeting human 5-lipoxygenase offers a strategy to diminish leukotriene-mediated inflammation and mitigate disease progression. Recent advances in computational biology significantly accelerate the selection of effective drugs by reducing the cost and time associated with conventional experimental screening. Molecular docking is a structure-based methodology that helps identify interaction patterns and binding affinities between bioactive compounds and proteins, thereby facilitating the identification of potential therapeutic agents for psoriasis (Senthilkumar et al., 2018). Therefore, in this work, various computational techniques were used to identify potential phytocompounds against the protein associated with psoriasis (Lionta et al., 2014). Furthermore, characterizing pharmacokinetic parameters through predictive ADMET modelling provides information on drug-likeness, oral bioavailability and toxicity profiles, improving the selection of lead molecules. In the present study, the ethanolic extract of Melia dubia fruit was characterised through qualitative screening and GC-MS analysis. Pharmacologically significant phytocompounds were docked against Human 5-Lipoxygenase (PDB ID: 3V99) using PyRx AutoDock Vina. The top-performing lead molecule was subjected to subsequent Swiss ADME. This integrated workflow reveals anti-psoriatic potential of Melia dubia for downstream experimental testing.

2. MATERIALS AND METHODS

1. 1. Collection and Preparation of Fruit Pulp:

Fresh fruits of Melia dubia were collected from Chennai district, Tamil Nadu, India. Fruits were washed with distilled water to remove surface debris. The fruit pulp was isolated manually and then shade-dried at room temperature for seven days (Azwanida, 2015). The dried material was then milled into a fine powder using a mechanical grinder and preserved in a sealed container. To ensure sample integrity handling at every stage of the process was performed under sterile conditions.

1. 2. Extraction of phytochemicals:

For the extraction of bioactive components, 50 g of powdered fruit flesh was macerated in 250 mL of 95% ethanol and subjected to Soxhlet extraction. The process was continued for 6–8 h until complete extraction was achieved. The obtained concentrate was aliquoted into vials and stored at 4ºC for further use.

1. 3. Phytochemical Analysis:

Phytochemical analysis is a preliminary step in the analysis of medicinal plants. These tests enable the identification of secondary metabolites present in the sample (Harborne, 1998). In the present work, the crude extract of Melia dubia underwent qualitative phytochemical tests to identify various compounds present. The major classes of secondary metabolites are alkaloids, flavonoids, tannins, glycosides, saponins, and steroids. The presence of phytocompounds was confirmed by chemical reactions in the sample, which resulted in colour changes, precipitate formation, and ring formation. Each test was performed under aseptic laboratory conditions (Trease & Evans, 2009).

2.4 GC-MS Analysis:

GC-MS is an analytical technique used to separate and identify volatile compounds. The volatile compounds are separated on the basis of their mass-to-charge ratios, generating mass spectra for identification (Harborne, 1998). The GC-MS analysis for this work was carried out at the Vellore Institute of Technology, Chennai, using an Agilent 7890A gas chromatograph coupled with a 5975C mass spectrometer. The sample was injected at temperature of 250ºC using a 1:10 split ratio. The mass spectra of the compounds were recorded and matched with NIST database to identify them (de Hoffmann & Stroobant, 2007).

1. 4. Ligand Preparation  

Ligand preparation is a crucial, automated process of converting the 2D molecules into accurate, high quality 3D structure for molecular docking. The phytocompounds obtained from the GC-MS analysis were used as ligands for docking studies (Morris et al., 2009). PubChem also helps study the physical and chemical properties of the ligands (Meng et al., 2011). In order to prevent the steric hindrance and to obtain the stable conformation, energy minimization of the ligands was carried out. Converting the ligands from PDB to PDBQT format was essential to guarantee computational compatibility during the simulation process.

1. 5. Protein Retrieval and Preparation:

The target protein, human 5-lipoxygenase, was retrieved from the Protein Data Bank (PDB) (RCSB PDB, 2025) in its 3D structure format. The protein retrieved from the PDB was subjected to refinement and preparation of protein before the docking process. Protein refinement was performed by removing the water molecules, co-crystallized ligands and other non-essential compounds to ensure proper docking of the protein with the selected ligand. This preparation of protein ensures the reliability of the docking results.

2.7 Molecular Docking:

Molecular docking was performed to identify the the interaction between the selected ligand and target protein. Molecular docking was carried out using AutoDock Vina (Eberhardt et al., 2021) and PyRx (Dallakyan & Olson, 2015). PyRx was used for docking. In this work, the selected phytocompounds from Melia dubia were used as ligands to interact with the target protein associated with psoriasis. The grid box was set up in the active-site region of protein to define the binding interactions of the ligands. The stable binding orientation of ligand and target protein was predicted based on binding-affinity values expressed in Kcal/mol. Lower binding-energy values indicate stronger and more stable interactions, whereas higher binding-energy values indicate weaker and less stable interactions between ligand and target protein (Morris & Lim-Wilby, 2008).

2.8 ADMET Analysis

ADMET analysis (Jiangyu Yan et al., 2021) was performed to identify the the pharmacokinetic and toxicity properties of the selected phytocompounds. ADMET represents the Absorption, Distribution, Metabolism, Excretion and Toxicity which are parameters used to predict the drug-likeness and toxicity of of the phytocompounds. In this work, the phytocompounds from Melia dubia that showed the best docking scores were selected and subjected to ADMET analysis. SwissADME was used for ADMET analysis. In this tool, the chemical structures of the selected phytocompounds were retrieved in SMILES format and uploaded. The compounds were analysed for pharmacokinetic properties to predict their potential as effective drug candidates for psoriasis. The obtained ADMET results were compared and interpreted with standard values to identify the phytocompounds with suitable pharmacokinetic properties for psoriasis (Lipinski et al., 2001). 

3. RESULTS

3.1 Phytochemical Analysis

Phytochemical analysis of Melia dubia revealed the presence of flavonoids, phenols, tannins, steroids, polyphenols and saponins. Glycosides and quinones were not detected. The rich content of flavonoids and phenolic compounds have a strong ability to bind and interact with the target protein. The presence of flavonoids, phenols and polyphenols have strong antioxidant properties whereas the presence of saponins enhances the medicinal value of the extract through its effective immunomodulatory, anti-inflammatory and membrane permeabilizing properties. Tannins show antimicrobial and anti-inflammatory properties. These findings suggest that Melia dubia may have potential for further investigation as an antipsoriatic agent.

Table 1: Interpretation of Phytochemical Analysis

Phytochemical Compounds	Result
Flavonoids	+
Phenols	+
Tannins	+
Steroids	+
Polyphenols	+
Saponins	+
Glycoside	-
Quinones	-

 

 

1         2         3        4      5      6      7    8     9   10

 

 

 

Fig. 2. GC-MS Analysis of Ethanolic Extract of Melia dubia

 

 

Fig 2- Graphical Representation of the Binding Affinity of the Ligands with Human 5-Lipoxygenase (Id: 3V99).

 

 

Fig. 4. Structure of Protein 5-Lipoxygenase (Id: 3V99).

 

 

Fig 5: Docking Analysis of the 5-lipoxygenase target protein associated with psoriasis (PDB Id: 3V99) with Betulin, a phytocompound present in Melia dubia

 

 

Fig 6: Docking Analysis of the 5-lipoxygenase target protein associated with psoriasis (PDB Id: 3V99) with Linoleic Acid, a phytocompound present in Melia dubia.

DISCUSSION 

Qualitative phytochemical screening and GC–MS profiling of the pigment extract obtained from Staphylococcus arlettae revealed the presence of several biologically relevant metabolites, including n-hexadecanoic acid, conjugated linoleic acid, octadecanoic acid, oleic acid derivatives, lanostane-type triterpenoids, lupeol derivatives, and phytol-related compounds. Similar classes of metabolites have previously been identified from microbial pigments and other natural products, where they have been associated with antioxidant, antimicrobial, and anti-inflammatory activities (Sasidharan et al., 2011; Bhardwaj et al., 2020). However, unlike previous studies that primarily investigated plant-derived metabolites, the present study demonstrates that pigment-producing bacteria isolated from the oral microbiota of Naja naja also constitute a promising source of structurally diverse bioactive compounds. The predominance of fatty acids and triterpenoid derivatives observed in the present investigation is consistent with earlier reports describing these metabolites as important contributors to microbial bioactivity. Similar occurrence of n-hexadecanoic acid has been reported in several bacterial and fungal extracts, where it has been associated with antimicrobial and anti-inflammatory properties (Bharathidhasan et al., 2015). Likewise, conjugated linoleic acid and oleic acid derivatives have previously been reported as naturally occurring lipid metabolites capable of modulating inflammatory responses and oxidative stress (Benjamin and Spener, 2009). The identification of these metabolites in the present pigment extract therefore supports the possibility that they collectively contribute to the observed biological activities rather than acting as isolated constituents. The detection of lanostane-type triterpenoids and a lupeol-related derivative further strengthens the pharmacological significance of the pigment extract. Similar triterpenoid compounds have been extensively reported from medicinal fungi and higher plants, where they exhibit anti-inflammatory, antioxidant, immunomodulatory, and anticancer properties through regulation of multiple inflammatory signalling pathways (Wasser, 2011; Saleem, 2009). Although lupeol has traditionally been described as a plant-derived pentacyclic triterpenoid, its identification in the present microbial pigment extract expands the chemical diversity associated with Staphylococcus arlettae and suggests that microbial pigments may represent an underexplored source of triterpenoid-like metabolites. The occurrence of a phytol-related diterpenoid alcohol is also in agreement with previous investigations demonstrating antioxidant, antimicrobial, and anti-inflammatory activities of phytol-containing natural extracts (Santos et al., 2013). The coexistence of fatty acids, diterpenoids, and triterpenoids within the same extract indicates a chemically diverse metabolite profile capable of producing complementary biological effects through multiple mechanisms rather than through a single dominant compound. Although phthalate ester derivatives were identified during GC–MS analysis, similar compounds have frequently been reported as contaminants originating from laboratory plasticware, solvents, or analytical instrumentation rather than authentic microbial metabolites (Biedermann et al., 2013). Therefore, these compounds should be interpreted cautiously and excluded from biological interpretation unless confirmed by additional analytical techniques. The present findings should also be interpreted within the limitations of GC–MS-based metabolite identification. Compound assignments were generated through comparison with the NIST spectral library and therefore represent putative identifications rather than definitive structural confirmation. Confirmation of the identified metabolites would require complementary analytical approaches such as LC–MS/MS, high-resolution mass spectrometry, or nuclear magnetic resonance spectroscopy. Furthermore, although many of the identified compounds have been individually reported to possess antioxidant, antimicrobial, and anti-inflammatory activities, the contribution of each metabolite within the complex pigment extract remains to be experimentally validated through purification, quantitative analysis, and mechanistic biological assays. Taken together, the present investigation demonstrates that the pigment-producing bacterium Staphylococcus arlettae isolated from the oral microbiota of Naja naja produces a chemically diverse metabolite profile enriched in biologically relevant fatty acids, triterpenoid derivatives, and diterpenoid compounds. While previous studies have largely focused on plant-derived sources of these metabolites, the present work identifies snake oral microbiota as a novel microbial reservoir of pigment-associated bioactive compounds. This expands current knowledge regarding microbial pigment chemistry and provides a scientific basis for future studies aimed at isolating individual metabolites and evaluating their therapeutic potential in antioxidant, anti-inflammatory, and antimicrobial applications.Bottom of Form

CONCLUSION

 The present study suggests that Melia dubia contains bioactive phytocompounds that may have therapeutic potential against the target protein associated with psoriasis. Phytochemical screening and GC-MS analysis revealed the presence of bioactive compounds with reported medicinal properties, including anti-inflammatory, anti-cancer and immunomodulatory activities. 5-lipoxygenase was selected as the target protein, and the identified ligands obtained through GC-MS were docked against it (Betulin, Oleic Acid, Lupeol, Linoleic acid, Palmitic Acid). The molecular docking results showed that betulin and linoleic acid exhibited favorable binding affinities. ADMET analysis suggested that both betulin and linoleic acid may have potential for further investigation as antipsoriatic candidates. This work helps to understand the basic and therapeutic potential of Melia dubia. As a future perspective, formulations such as topical creams, gels, and nanoformulations can be developed for drug delivery purposes. Molecular dynamics simulations can be carried out to determine the stability and behaviour of protein–ligand complexes over time. In vitro and in vivo studies can be performed to evaluate the efficacy and therapeutic applications of phytocompounds from Melia dubia in keratinocytes and immune cells under physiological conditions. From this we can conclude that, this work acts as the starting point for the development of drug by a phytocompound present in Melia dubia for psoriasis. 

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