Abstract This study explores the potential of Ailanthus excelsa Roxb. for managing obesity by evaluating its effects on key metabolic enzymes. We evaluated a hydroalcoholic extract and its fractions for their ability to modulate important metabolic enzymes, porcine pancreatic lipase, HMG-CoA reductase, α-glucosidase, and α-amylase activities. Our methodology integrated in vitro enzymatic assays with cluster analysis (MCODE, ClueGO, and Cluepedia) and network pharmacology to elucidate interactions between metabolites and target enzymes. Protein-protein interaction (PPI) analysis, consisting of a network with 51 nodes and 264 edges, was performed using the CytoNCA plugin to calculate topological parameters. Key targets were identified based on degree centrality, including ADIPOQ, PPARA, PPARG, IL6, TNF, and AKT1. Cluster analysis of the PPI networks, conducted using the MCODE plugin, highlighted a top cluster with a high score of 22.82. Network pharmacology has identified key targets associated with obesity, including HK1, HK2, PIK3CA, AKT1, MTOR, CD36, ACACB, SLC2A4, CPTIA, INSR, ACACA, FASN, and ADIPOQ. These targets are linked to highly modulated metabolic pathways. Isoquercetin shows significant binding affinities: − 7.11 for HMG-CoA Reductase (PDB ID: 1HW9), -9.96 for lipase (PDB ID: 1LPB), − 8.96 for α-amylase, and − 10.41 for α-Glucosidase (PDB ID: 3A47). The ethyl acetate fractions exhibit notable inhibition of Porcine Pancreatic lipase (IC[50]: 56.25 ± 4.85 µg/mL) and HMG-CoA reductase (IC[50]: 108.27 ± 3.38 µg/mL), α-glucosidase (IC[50]: 117.08 ± 3.28 µg/mL), and α-amylase (IC[50]: 125.93 ± 2.29 µg/mL). Moreover, metabolites showed stronger binding affinities to all four enzymes than reference molecules. By integrating in vitro assays with molecular modeling, this study highlights the promising potential of A. excelsa and its fractions in obesity management, offering valuable insights into its therapeutic applications. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-025-14420-2. Keywords: Ailanthus excelsa Roxb, Cluster analysis, Molecular dynamic simulation, α-glucosidase Subject terms: Computational biology and bioinformatics, Drug discovery Introduction Obesity, a global health crisis, has become one of the most pressing public health challenges of the 21st century^[40]1. Defined by excessive fat accumulation, obesity significantly increases the risk of metabolic diseases such as hypertension, type 2 diabetes, and dyslipidaemia. The prevalence of obesity has surged worldwide, affecting both adults and children. According to the World Health Organization (WHO), over 650 million adults were obese in 2016, a staggering increase since 1975^[41]2. This dramatic rise is primarily driven by urbanization, sedentary lifestyles, and unhealthy diets, coupled with an aging population^[42]3. Obesity’s role as a precursor to type 2 diabetes mellitus (T2DM) is particularly concerning. T2DM, which accounts for most diabetes cases, often stems from insulin resistance, where changes in receptor structure reduce hormone-receptor affinity or impair insulin secretion. In contrast, type 1 diabetes mellitus arises from a complete disruption in insulin secretion^[43]4. The International Diabetes Federation (IDF) reported that 537 million adults were living with diabetes in 2021, with 6.7 million deaths attributed to the disease. The burden of diabetes is expected to escalate further, with projections indicating that 643 million people will be affected by 2030 and 783 million by 2045, further compounding the global health crisis^[44]5. Given the strong connection between obesity and T2DM, effective strategies to manage both conditions are crucial^[45]6. One promising approach involves inhibiting enzymes responsible for carbohydrate digestion, such as α-amylase and α-glucosidase^[46]7. These enzymes hydrolyze α-1,4-glycosidic bonds in carbohydrates, such as starches, producing absorbable monosaccharides. Inhibiting α-amylase and α-glucosidase slows carbohydrate digestion, thereby reducing postprandial glucose levels and contributing to the management of both diabetes and obesity^[47]8. Furthermore, inhibiting lipase and HMG-CoA reductase enzymes play a key role in regulating lipid metabolism, offering additional therapeutic benefits in managing obesity and its related complications. In addition to these enzymatic pathways, oxidative stress is a significant complication associated with diabetes and obesity. Oxidative stress arises from an imbalance between reactive oxygen species (ROS) production and the body’s antioxidant defence mechanisms^[48]9. This imbalance leads to cellular damage and is implicated in the progression of chronic diseases, including diabetes and cardiovascular disease^[49]10. While conventional pharmaceutical treatments for diabetes and obesity are available, they often come with limitations, such as side effects and long-term safety concerns. Oral drugs, for instance, may be useful for individuals who are allergic to insulin or prefer not to use insulin injections^[50]11. However, prolonged use of these medications can increase the risk of heart attacks, acute kidney injury, and liver toxicity^[51]12. Consequently, there is a growing interest in developing traditional medicines that offer a safer and more sustainable alternative for managing these conditions^[52]13. Traditional medicines, derived from natural sources, have long been used to treat various ailments and are considered a valuable reservoir of bioactive compounds with therapeutic potential. In this context, A. excelsa, a versatile medicinal plant, has garnered attention for its potential anti-obesity, anti-diabetic, and antioxidant properties. Commonly known as the “tree of heaven,” A. excelsa belongs to the Simaroubaceae family and is native to Asia, Africa, and Australia^[53]14. Historically, different parts of the A. excelsa tree, including its bark, leaves, and roots, have been utilized in traditional herbal medicine for their purported medicinal properties^[54]15. These include anti-asthmatic, hepatoprotective, and hypoglycaemic effects. However, the potential impact of A. excelsa extract on obesity and its mechanisms of action remains largely unexplored^[55]16. This study explores the potential of A. excelsa as a therapeutic agent for managing obesity and related metabolic disorders. By investigating the Pharmacognostical properties and metabolite profiles of its hydroalcoholic extract, the research evaluates its anti-obesity, anti-diabetic, and antioxidant activities through in vitro assays. The integration of computational techniques, such as network pharmacology and molecular modeling, provides insights into the molecular interactions of the plant’s bioactive compounds. This study aims to contribute to traditional medicine by highlighting the therapeutic potential of A. excelsa and its relevance in developing safe, plant-based treatments for chronic diseases like diabetes and obesity. Specifically, this study addresses the limited exploration of Ailanthus excelsa as a potential therapeutic agent for obesity and metabolic disorders. Although traditional uses of A. excelsa have been documented, its mechanisms of action, particularly in targeting key metabolic pathways such as PPAR and PI3K-Akt signaling, remain understudied. The integration of network pharmacology, molecular docking, and in vitro assays offers a comprehensive approach to elucidate these mechanisms. By focusing on lipid modulation, enzyme inhibition, and antioxidant activities, this research provides new insights into the plant’s bioactive compounds, addressing gaps in both Pharmacognostical profiling and therapeutic evaluation. Methods Collection of plant material The plant material of Ailanthus excelsa was collected in June from the Hidakal Dam region, Belagavi. This species is not listed under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) or any other endangered species lists. The collection was conducted in accordance with the Plant Protection Act (PPA) and the International Plant Protection Convention (IPPC) guidelines, ensuring that no harm was caused to any endangered flora. Sustainable harvesting practices were strictly followed throughout the process. The plant was identified and authenticated by a qualified taxonomist at the Indian Council of Medical Research (ICMR) – National Institute of Traditional Medicine (NITM), and assigned the authentication reference number RMRC-1715. A voucher specimen has been deposited in the herbarium of ICMR-NITM for future reference. Following collection, the plant parts were manually separated and air-dried under shade on a muslin cloth for 10–15 days. After complete drying, the material was ground into a coarse powder for further processing. Standardization parameters and physicochemical evaluation By the guidelines of the Indian Pharmacopeia and Herbal Pharmacopeia, physicochemical characteristics such as acid-insoluble ash, total ash, water-soluble ash, and extractive values were investigated. They were assessing the ash content aids in identifying low-quality products, exhausted drugs, and the presence of excessive sand or other earthy materials. Microscopic characteristics of powdered plant substances were observed in scanning electron microscopy. This method is essential for quality control, identification of species, and detection of contaminants in herbal medicines and spices. Preparation of plant extract and fractions The crude drug was thoroughly washed, cut into small pieces, and shade-dried before being coarsely powdered. The coarse powder was then extracted using a hydroalcoholic solvent (70:30) through the maceration technique. After extraction, the solvent was evaporated under reduced pressure using a rotary vacuum evaporator, and the resulting extract was stored in an airtight container for further use. A portion of the extract was suspended in distilled water and subjected to successive liquid-liquid partitioning with n-hexane, ethyl acetate, chloroform, and petroleum ether to obtain different fractions^[56]17. Preliminary phytochemical screening Preliminary phytochemical screening helps identify the secondary metabolites present in plants carried out by previously reported methods^[57]18. Quantitative analysis (Hydro alcohol, Ethyl acetate and hexane) Determination of total phenol content (TPC) The total phenol content in the plant extracts was determined using the Folin-Ciocalteu method, with gallic acid as the standard, incorporating slight modifications. The reaction mixture consisted of 1 ml of the extract and 9 ml of distilled water. Subsequently, 1 ml of Folin-Ciocalteu phenol reagent was added, and the mixture was shaken well. After 5 min, 10 ml of a 7% sodium carbonate solution was added. Standard solutions of gallic acid were prepared at concentrations of 20, 40, 60, 80, and 100 µg/ml. The mixture was incubated for 90 min at room temperature, and the absorbance of the test and standard solutions was measured against a reagent blank at 550 nm using an ultraviolet (UV)/visible spectrophotometer. The total phenol content was expressed as mg of gallic acid equivalents (GAE) per gram of extract^[58]19. Determination of total flavonoid content (TFC) According to Martínez S et al.^[59]20, the total flavonoid content in the plant extract was determined using the aluminium chloride method. The reaction mixture consisted of 0.25 ml of plant extract in 1.25 ml of distilled water, followed by the addition of NaNO[3]. The mixture was placed in the dark for 6 min, after which 0.15 ml of 10% AlCl[3] was added and incubated for an additional 15 min. Subsequently, 0.5 ml of NaOH and 0.275 ml of distilled water were added to the mixture. Standard solutions of quercetin were prepared at concentrations of 20, 40, 60, 80, and 100 µg/ml. The absorbance of the standard and extract solutions was measured against a reagent blank at 510 nm using a UV/Visible spectrophotometer. The total flavonoid content was determined from the calibration curve and expressed as milligrams of quercetin equivalent (QE) per gram of extract. Determination of total alkaloid content (TAC) The plant extract (1 mg) was dissolved in dimethyl sulfoxide (DMSO) and then acidified with 1 mL of 2 N hydrochloric acid (HCl). The resulting solution was filtered and transferred to a separating funnel. Subsequently, 5 mL of bromocresol green solution and 5 mL of phosphate buffer were added. The mixture was subjected to vigorous shaking with chloroform, and the organic phase was collected in a 10-mL volumetric flask. The volume was then adjusted to the mark with chloroform. For calibration, a series of reference standard solutions of atropine (20, 40, 60, 80, and 100 µg/mL) were prepared using the same procedure. The absorbance of both test and standard solutions was measured at 470 nm using a UV/Visible spectrophotometer, with the reagent blank as the reference. The total alkaloid content was expressed as mg of atropine equivalent (AE) per gram of extract^[60]21. Biological evaluation Determination of antioxidant activity and free radical scavenging activities The radical scavenging activity of the extracts was studied using DPPH free radical assay, ferrous ion chelating, nitric oxide scavenging activity, ABTS radical scavenging activity, and total antioxidant activity by phosphomolybdenum method were determined according to established methods^[61]22,[62]23. Determination of Porcine pancreatic lipase Inhibition assay Porcine pancreatic Lipase Inhibition activity was carried out by Andersone et al.^[63]24 method with slight modification. A stock solution of A. excelsa extract and standard were prepared. Serial dilution of extract and standard were prepared in the range of (20–100 µg/ml). Collect different test tubes and label them as samples (hydro alcohol extract and n-hexane, petroleum ether, chloroform, and ethyl acetate fractions). In the sample tube, add 1 ml extract and 0.5 ml lipase solution. Incubate for 30 min. Then, add the PNPB substrate, and continue incubation for 30 min. After that, absorbance was recorded at 410 nm. Orlistat was used as a standard and formed in the same manner as the sample. α-amylase Inhibition assay The study aimed to evaluate the inhibitory potency of A. excelsa extract against the α-amylase enzyme. The α-amylase inhibition properties of samples were performed as described in Tian et al.^[64]25. α-amylase (3 units/mL) was dissolved in 0.1 M buffered phosphate-buffered saline, pH 6.9. Samples at various concentrations (0–100 µg/mL) were pre-incubated with the enzyme for 10 min at 37 °C. The reaction commenced upon adding substrate (0.1% starch) to the incubation medium. After 10 min, the reaction was halted by adding 250 µL of dinitro salicylic (DNS) reagent (comprising 1% 3,5-dinitro salicylic acid, 0.2% phenol, 0.05% Na[2]SO[3], and 1% NaOH in aqueous solution), followed by boiling the reaction mixture for 10 min in a water bath. Subsequently, 250 µL of 40% potassium sodium tartrate solution was added. After cooling to room temperature in a cold-water bath, the absorbance was measured at 540 nm. α-Glucosidase inhibition assay The α-glucosidase inhibitory activities of samples were evaluated using the method and Kifle ZD et al.^[65]26. α-glucosidase was dissolved in phosphate buffer (50 mM, pH 6.9) and treated with different concentrations of samples (0–100 µg/mL) individually for 10 min at 37 °C. The reaction commenced with adding 50 µL of 5 mM p-nitrophenyl-α-D glucopyranoside in phosphate buffer. The enzyme reaction proceeded at 37 °C for 30 min. The reaction was terminated by adding Na[2]CO[3] (1 M), followed by measuring the absorbance at 405 nm. HMG-CoA reductase inhibition assay The inhibitory effect of various samples on HMG-CoA reductase was evaluated using a modified method from Baskaran et al.^[66]27. Each sample was tested at concentrations ranging from 25 to 125 µg/mL, mixed with a reaction solution containing nicotinamide adenine dinucleotide phosphate (400 µM), HMG-CoA substrate (400 µM), and potassium phosphate buffer (100 mM, pH 7.4) with potassium chloride (120 mM), ethylene diamine tetra acetic acid (1 mM), and dithiothreitol (5 mM). HMG-CoA reductase (2 µL) was added, and the mixture was incubated at 37 °C. Absorbance was measured at 340 nm after 10 min. Simvastatin (Sigma-Aldrich Co.) was a positive control, and distilled water was used as a negative control. Using a positive control, the percentage of inhibition was determined using the following formula for Porcine pancreatic Lipase, α-amylase, α-glucosidase, and HMG-CoA reductase inhibition assay: (OD of blank-OD of test/OD of Blank) * 100. The results were represented in IC[50] values. All in vitro experiments were performed in triplicate (n = 3) to ensure reproducibility and reliability of results. Data were expressed as mean ± standard deviation (SD). The IC[50] values were calculated using non-linear regression analysis. Computer-aided studies Identification of active components of Ailanthus excelsa and target retrieval The biologically active phytochemicals present in Ailanthus excelsa were identified through a comprehensive literature review and public repositories, including Dr. Duke’s Phytochemical and Ethnobotanical Database (Dr. Duke’s DB), IMPPAT database and PubChem ([67]https://pubchem.ncbi.nlm.nih.gov/) database. The potential molecular targets of these phytoconstituents were predicted using DIGEP-pred, SwissTargetPrediction, and SuperPred databases. Additionally, obesity-related targets were retrieved from multiple databases, including DisGeNET ([68]https://www.disgenet.org/browser/0/1/0/C0028754/), the Therapeutic Target Database ([69]https://db.idrblab.net/ttd/), and Gene Cards ([70]https://www.genecards.org/). Ailanthus excelsa - obesity common target network construction A venny 2.0 intersect the common targets between A.excelsa-Obesity. After that, import the common targets into Cytoscape to build the A. Excelsa-Obesity shared target network. Analysis of the main targets and bioactive components of A. excelsa against Obesity according to the degree. Protein-protein interaction Constructing protein-protein interaction (PPI) networks for common targets between the compounds and disease targets were visualized using the STRING database. PPI data were subsequently exported to Cytoscape for further analysis of centrality measures. In these networks, nodes represented targets, while edges depicted interactions between the targets. The platform assessed the mutual information score for each protein, where a higher score indicated stronger interactions between targets. Isolated targets were excluded from the study, and the PPI network was constructed with a confidence score threshold of 0.04. Subsequently, key topological properties were analyzed, including degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), eigenvector centrality (EC), information centrality (IC), local average connectivity-based method (LAC), network centrality (NC), and subgraph centrality (SC) using the CytoNCA plugin in Cytoscape^[71]28. These metrics were employed to identify core targets within the network. Finally, cluster analysis was performed using the MCODE clustering module in Cytoscape 3.10.2, with the clustering coefficient set to identify three distinct clusters. GO and KEGG pathway enrichment analyses of PPI network and cluster for obesity using clue GO and Clue Pedia plugins Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the ClueGO and CluePedia plugins within the Cytoscape software environment. GO terms related to Biological Process (BP), Molecular Function (MF), and Cellular Component (CC) categories were selected for functional annotation (GO database: [72]www.geneontology.org; KEGG: [73]www.kegg.jp/kegg/kegg1.html). ClueGO ([74]https://apps.cytoscape.org/apps/cluego) was used to visualize and functionally group enriched GO terms and KEGG pathways, facilitating the interpretation of complex gene-function relationships. To enhance the analysis, CluePedia ([75]https://apps.cytoscape.org/apps/cluepedia) was integrated with ClueGO, enabling deeper exploration of gene–pathway interactions and identification of potential novel biomarkers. Further SRplot: A free online platform was used for data visualization and graphing ([76]https://www.bioinformatics.com.cn/en). This combined approach provided a systems-level understanding of the functional associations and biological significance of the gene dataset^[77]29,[78]30.35. Network construction and analysis Cytoscape 3.10.2 created a network connecting the phytocompounds of A. excelsa with their respective targets. This network visualized the interactions between the active constituents and target genes. Using the “Network Analyzer” tool as a direct command, edge count was prioritized from high too low for modulation. Additionally, network analysis was conducted based on “Node degree distribution” and “Betweenness by degree,” considering parameters such as eccentricity, neighbourhood connectivity, in-degree distribution, and outdegree distribution. In this network construction, nodes represented the components, targets, and pathways, while edges depicted the interactions among these factors. This representation elucidated the relationship between the active ingredients and disease targets. The degree value of interactions was used to assess the importance of nodes in each network^[79]31. Molecular docking To investigate the binding interaction and orientation of 31 phytoconstituents as inhibitors in the α-amylase, α-glucosidase, porcine pancreatic Lipase and HMG-CoA pocket, molecular docking study was taken into consideration using Schrodinger’s glide extra precision mode (XP)^[80]32 Using Maestro, all of the identified ligand structures were represented^[81]33. Ligprep in Schrödinger’s suite was used for ligand construction, employing OPLS4 for energy minimization. Torsional flexibility was applied to enhance pose complementarity. Crystal structure coordinates of the α-amylase (PDB ID: 4W93), α-glucosidase (PDB ID: 3TOP), Porcine pancreatic Lipase (PDB ID: 2OXE) and HMG-CoA (PDB ID: 1HW9) were retrieved from a protein data bank ([82]https://www.rcsb.org). The proteins underwent pre-processing, which involved deleting ligands and water molecules from the PDB dataset, assigning bond orders, and generating PKa values at PH 7 ± 2. The protein was further refined by energy reduction using an OPLS4 force field to achieve a stable structure for more analysis. A. A co-crystal ligand was used to construct a grid to identify the binding location inside the target receptor. The binding affinity of ligands with receptors was described regarding docking score, hydrogen bonds, and pi-pi interactions using Glide software in extra precision (XP) mode. Molecular dynamics (MD) simulations Molecular dynamics (MD) simulations were conducted using the Desmond Molecular Dynamics System (version) for 100 ns. The receptor-ligand complexes (Isoquercetin-HMG-CoA and Isoquercetin-Lipase) were solvated in a cubic TIP3P water box with 10 Å side lengths. System preparation included neutralizing the net charge and achieving an ionic strength of 0.15 M with salt addition to maintain electroneutrality. Simulations employed the Smooth Particle Mesh Ewald (SPME) algorithm for accurate short-range non-bonded interactions with a 9 Å cutoff and efficiently handled long-range electrostatics. Initial equilibration simulations of 10 ns validated system suitability, followed by a multi-stage relaxation protocol in an NPT ensemble to prepare equilibrated structures. The protocol included restrained minimization (two rounds of 2000 steps/round) with 50 kcal/mol/Ų harmonic restraints on solute atoms, followed by four MD stages: (1) 12 ps of NVT ensemble at 10 K with constant volume, (2) 12 ps of NPT ensemble at 10 K, (3) 24 ps of NVT ensemble with temperature ramped to 300 K, and (4) 24 ps of NPT ensemble at 300 K with unrestrained MD. Subsequently, two phases of relaxation were performed: a brief 1.2 ns phase and a longer unrestrained 10 ns phase, with a Nose-Hoover thermostat maintaining 310 K temperature and pressure controlled isotropically using a Martyna-Tobias-Klein barostat. Periodic boundary conditions and the multistep RESPA integrator were consistently applied throughout. The MD trajectories were analyzed using the Desmond software suite to assess system stability and molecular interactions^[83]5,[84]34. Results and discussion Pharmacognostical evaluation Standardization parameters By evaluating the ash levels, it is easy to determine where the powdered material was contaminated with sand and other inorganic material. The quantity of inorganic material contained in the crude medication may be determined using the water-soluble ash (3.31 ± 0.25). In contrast, the amount of sand and other debris can be determined using the in acid-insoluble ash (2.05 ± 0.33) and sulphated ash was found to be 2.1 ± 0.47. The varying extraction values using various solvents have been identified. Alcohol has the highest extractive value (6.44 ± 0.42), followed by water (3.24 ± 0.53), Hexane (3.54 ± 0.12), ethyl acetate (2.88 ± 0.32), petroleum ether (2.32 ± 0.95) and chloroform (2.04 ± 0.83). The extractive values play a role in determining the best solvent to utilize for extracting the most active principle (Table [85]S1). Powder microscopy Powder microscopy of A. excelsa revealed distinct cellular components, including sclereids, fibers, cork cells, calcium oxalate crystals, medullary rays, and xylem cells. They were scanning electron microscopy images (Fig. [86]1). Showed fibers grouped, characterized by their relatively large size, thin walls, and numerous pits. Sclereids were identified as lignified, thick-walled, rectangular cells in clusters. Thin-walled, colorless cork cells were also observed. The sample contained minute, needle-shaped acicular raphides and idioblasts of calcium oxalate crystals. Medullary rays varied from biseriate to tetraseriate, with some being uniseriate. Xylem vessels were abundant, exhibiting bordered pitting, and often associated with other xylem elements. Starch grains were primarily simple and oval, with both single and compound forms present. Fig. 1. [87]Fig. 1 [88]Open in a new tab Scanning electron micrographs of Ailanthus excelsa bark powder. Preliminary phytochemical screening The preliminary phytochemical screening of A. excelsa extract revealed the presence of various secondary metabolites, including alkaloids, phenols, tannins, steroids, triterpenoids, flavonoids, and glycosides, as detailed in Table S2. Total phenol, flavonoid, and tannin content estimations In a comparative study of sample and fractions, it was found that Ethyl acetate fraction exhibited the highest concentrations of polyphenols, flavonoids and alkaloids among the tested samples. Specifically, Ethyl acetate fraction revealed the highest content of total polyphenols (82.39 ± 2.13 mg GAE/g), flavonoids (95.24 ± 3.21 mg QE/g), and alkaloids (185.31 ± 1.42 mg AT/g) (Table [89]1). Table 1. Results of total phenol, flavonoid, and tannin contents. Hydro alcohol Ethyl acetate** N- Hexane** TAC (mg AT/g) 148.86 ± 3.96 185.31 ± 1.42 156.96 ± 2.95 TPC (mg GAE/g) 67.97 ± 4.97 82.39 ± 2.13 54.97 ± 5.17 TFC (mg QE/g) 79.43 ± 2.31 95.24 ± 3.21 65.98 ± 3.92 [90]Open in a new tab Showing mean ± S.D (n = 3), ** Fractions. In-vitro studies In-vitro antioxidant activity The assessment of antioxidant activity in the hydroalcoholic extract and fractions of A. excelsa involves various tests. The efficacy of plant extracts in combating free radicals is contingent upon their composition and the testing conditions. Antioxidant capacities are subject to numerous influencing factors, necessitating the use of multiple assays to comprehensively assess the diverse mechanisms of antioxidant action. The ethyl acetate fraction and hydroalcoholic extract exhibited notable free radical scavenging activity. Both ethyl acetate fraction and standard substances demonstrated increasing inhibition values with concentration. Table [91]2. provides the IC[50] values for Ailanthus excelsa in various antioxidant tests. Table 2. The IC[50] values for the antioxidant properties of the Ailanthus excelsa extract and fractions were determined using various methods. Samples DPPH (µg/ml) Phosphomolybdenum (µg/ml) Ferrous Ion (µg/ml) NO Scavenging (µg/ml) ABTS (µg/ml) AE Extract 43.90 ± 3.3 85.59 ± 2.4 94.51 ± 6.6 95.86 ± 2.5 73.96 ± 2.7 Ethyl acetate** 38.38 ± 2.92 73.30 ± 4.5 72.87 ± 2.4 76.97 ± 3.3 59.98 ± 4.2 Chloroform** 156.42 ± 5.8 109.27 ± 3.6 183.01 ± 4.7 121.97 ± 3.9 107.35 ± 3.8 Petroleum Ether** 68.58 ± 1.6 106.80 ± 5.8 147.60 ± 2.4 128.2 ± 4.4 113.86 ± 2.1 N-hexane** 41.64 ± 3.5 84.51 ± 1.3 82.79 ± 1.1 116.97 ± 2.8 96.97 ± 3.02 Std (5–25 µg/ml) 13.93 ± 0.7 (AA) 29.35 ± 1.4 (EDTA) 62.85 ± 2.32 (AA) 64.98 ± 1.2 (AA) 25.84 ± 2.3 (BHA) [92]Open in a new tab Showing mean ± S.D (n = 3), ** Fractions. Porcine pancreatic lipase Inhibition assay The inhibitory effects on porcaine pancreatic lipase were assessed using PNPB as the substrate, with different concentrations of both standard and A. excelsa extract and fractions being evaluated. The hydroalcoholic extract of A. excelsa exhibited significant inhibition of pancreatic lipase with an IC[50] value of 97.92 ± 2.37 µg/mL, while the ethyl acetate fraction showed superior inhibitory activity with an IC[50] value of 56.25 ± 4.85 µg/mL. The n-hexane fraction demonstrated moderate activity (IC[50]: 106.84 ± 3.96 µg/mL), but chloroform and petroleum ether fractions showed no significant inhibition (NA). The inhibition profile of ethyl acetate was notable, as opposed to the standard orlistat (IC[50]: 49.86 ± 4.37 µg/mL). This suggests that specific components within the ethyl acetate fraction may contribute to enhanced lipase inhibition. Figure [93]2a bargraph reprrsents the IC[50]value of Porcine Pancreatic Lipase Inhibition. Fig. 2. [94]Fig. 2 [95]Open in a new tab IC[50] values for enzyme inhibition. (a) Porcine pancreatic lipase inhibition (b) HMG-CoA reductase (c) α-amylase inhibition (d) α-glucosidase inhibition. HMG-CoA reductase inhibitory activity HMG-CoA reductase inhibitory activity was done by standard protocol, findings revealed Inhibition of HMG-CoA reductase, a critical enzyme in cholesterol biosynthesis, was most effective with the ethyl acetate fraction (IC[50]: 108.27 ± 3.38 µg/mL), followed by the A. excelsa extract (IC[50]: 117.92 ± 4.92 µg/mL). The n-hexane fraction showed weaker inhibition (IC[50]: 138.27 ± 2.47 µg/mL), while chloroform and petroleum ether fractions demonstrated no significant activity (NA). Simvastatin, used as a reference, inhibition (IC[50]: 45.92 ± 1.84 µg/mL), indicating that while A. excelsa and its fractions possess moderate HMG-CoA reductase inhibitory activity. Figure [96]2b bargraph reprrsents the IC[50] value of HMG-CoA reductase inhibitory activity. Nevertheless, the ethyl acetate fraction’s effectiveness suggests the presence of bioactive compounds with potential lipid-lowering effects, results are represented in Table [97]3. Table 3. The IC[50] values for Porcine pancreatic Lipase, HMG coa reductase, α-amylase and α-glucosidase inhibitory activity. Samples Porcine Pancreatic lipase HMG-CoA reductase α-amylase α-glucosidase Ailanthus excelsa Extract 97.92 ± 2.37 117.92 ± 4.92 139.63 ± 4.21 132.97 ± 2.23 Ethyl acetate* 56.25 ± 4.85 108.27 ± 3.38 125.93 ± 2.29 117.08 ± 3.28 Chloroform* NI NI 154.32 ± 4.94 153.08 ± 2.86 Petroleum Ether* NI NI 165.94 ± 3.72 148.38 ± 4.32 N-hexane* 106.84 ± 3.96 138.27 ± 2.47 134.82 ± 3.37 128.42 ± 4.63 Orlistat 49.86 ± 4.37 – – – Simvastatin – 45.92 ± 1.84 – – Acarbose – – 28.73 ± 2.97 39.72 ± 3.52 [98]Open in a new tab Showing mean ± S.D (n = 3), ** Fractions, NI: No Inhibition. α-amylase inhibition The inhibition percentages of α-amylase for one extract and four fractions were calculated relative to acarbose. The ethyl acetate fraction displayed the highest inhibition of α-amylase (IC[50]: 125.93 ± 2.29 µg/mL), followed by the n-hexane fraction (IC[50]: 134.82 ± 3.37 µg/mL) and the A. excelsa extract (IC[50]: 139.63 ± 4.21 µg/mL). The chloroform and petroleum ether fractions exhibited weaker inhibitory effects with IC[50] values of 154.32 ± 4.94 µg/mL and 165.94 ± 3.72 µg/mL, respectively. Acarbose, the standard α-amylase inhibitor, demonstrated a significantly stronger inhibition (IC[50]: 28.73 ± 2.97 µg/mL). Figure [99]2c shows the IC[50] values for α-amylase inhibition. Although the plant fractions are less effective than acarbose, the ethyl acetate fraction’s activity is noteworthy, indicating potential for carbohydrate digestion modulation. . α-glucosidase Inhibition Evaluating the percentage inhibition of α-glucosidase for one extract and four fractions. Similar trends were observed in the inhibition of α-glucosidase, with the ethyl acetate fraction showing the highest activity (IC[50]: 117.08 ± 3.28 µg/mL), followed by the A. excelsa extract (IC[50]: 132.97 ± 2.23 µg/mL). The n-hexane fraction also exhibited moderate inhibition (IC[50]: 128.42 ± 4.63 µg/mL), while the chloroform and petroleum ether fractions were less effective, with IC[50] values of 153.08 ± 2.86 µg/mL and 148.38 ± 4.32 µg/mL, respectively. Acarbose, as the standard, had an IC[50] value of 39.72 ± 3.52 µg/mL, indicating a much stronger inhibition compared to the plant fractions. However, the ethyl acetate fraction’s inhibition of α-glucosidase is promising for controlling postprandial hyperglycemia. Figure [100]2d shows the IC50 values for α-glucosidase inhibition. The ethyl acetate fraction consistently showed the highest inhibition across all four metabolic enzymes, suggesting it contains potent bioactive compounds. While the inhibition of pancreatic lipase and HMG-CoA reductase was notable, these values are still higher compared to reference standards such as orlistat and simvastatin. However, the combination of moderate inhibition across multiple enzymes indicates that A. excelsa and its fractions may offer a holistic approach to managing obesity through the simultaneous modulation of lipid and carbohydrate metabolism. Further isolation and characterization of the active compounds from the ethyl acetate fraction could lead to the development of effective multi-target therapeutic agents. Network pharmacology Ailanthus excelsa component-target network The components of A. excelsa were obtained from Dr Duke, IMPPAT and Published articles, a total of 31 bioactive components were obtained. The chemical information of all 31 components given in (Table S3). Action targets for these 31 bioactive components were predicted using Digep pred, Swiss target prediction and super pred databases. After removing duplicates in total, 838 targets of from Digep pred, 705 targets from Swiss target prediction and 365 targets from super pred databases were predicated (Fig. [101]3a). The A.s excelsa component target network comprised 1581 nodes and 34493 edges, 43.6 average node degree, 0.381 avg. local clustering coefficient, 23017 expected number of edges and < 1.0e-16 PPI enrichment p-value (Fig. [102]S1). With Apigenin (degree = 561), 3-hydroxyphenyl valeric acid (degree = 228), Cinnamic acid (degree = 106), Caftaric acid (degree = 84), Quinic acid (degree = 73), 3, 4 Dihydroxy phenylacetic acid (degree = 58), Canthin-6-one (degree = 58) identified as the primary bioactive components (Fig. S2). “The values of SUID, Average Shortest Path Length, Betweenness Centrality, Closeness Centrality, Clustering Coefficient, Degree, Layout, Eccentricity, Edge Count, In-degree, Component Name, Out-degree, Partner of Multi-edged Node Pairs, and Self-loops for 31 bioactive components are provided in Table S4. Fig. 3. [103]Fig. 3 [104]Open in a new tab (a) Common targets representation of digep pred, Swiss target prediction and super pred databases. (b) The venn diagram representation of common genes between AE components and Obesity related targets. Selection of disease (Obesity) related targets To achieve a comprehensive collection of obesity-related targets, data were gathered from several key databases. Specifically, DisGeNET ([105]https://www.disgenet.org/browser/0/1/0/C0028754/), which compiles gene-disease associations, was utilized. The Therapeutic Target Database (TTD, [106]https://db.idrblab.net/ttd/) contributed 802 targets related to obesity, offering detailed information on therapeutic proteins, gene targets, associated diseases, pathways, and relevant drugs. Gene Card ([107]https://www.genecards.org/) provided an extensive set of 10,019 obesity-related targets covering various aspects such as genomics, transcriptomics, proteomics, genetics, clinical data, and functional annotations. Additionally, 22 targets were sourced from the Pharmacogenomics Knowledgebase (PharmGKB, [108]https://www.pharmgkb.org/), which focuses on the interplay between actionable genes and clinical drug responses. Following the removal of duplicate entries, a consolidated set of 546 unique obesity-related targets was established. Intersection of AE components -obesity common-target network The intersection of A. excelsa components and obesity-related targets identified 255 common targets (Fig. [109]3b). The resulting network, which consists of 255 nodes and 4,619 edges includes 28 bioactive components of A. excelsa (Fig. [110]4). The main targets and bioactive components were analyzed based on their degree values, which represent the number of connections each node has within the network. The results highlighted that Apigenin (degree = 67), with the highest number of connections, plays a central role, indicating its significant interaction with obesity-related targets. 3-Hydroxyphenyl valeric acid (degree = 32) and Quinic acid (degree = 18) also showed considerable connectivity, suggesting their importance. Other components such as Caftaric acid (degree = 16), Canthin-6-one (degree = 14), 3,4-Dihydroxyphenylacetic acid (degree = 12), Oleanolic acid (degree = 12), Selinidin (degree = 12), and Malic acid (degree = 9) were identified as critical bioactive compounds due to their moderate degree values, reflecting their roles in the network. In contrast, Salicylic acid, Protocatechuic acid, and Glaucarubine were found to have no common targets with the obesity-related disease targets, as indicated by their degree values of zero. Fig. 4. [111]Fig. 4 [112]Open in a new tab Ailanthus excelsa Roxb components targets and obesity related common target network. Protein-Protein interaction of AE- obesity targets The 255 common targets were imported into String database, and then unconnected nodes like NUCB2 and IRAK1BP1 target was discarded. The PPI network included 225 nodes and 4619 edges. After that PPI network was exported to Cytoscape 3.10.1 for further analysis. The topological parameters of the A. excelsa -Obesity PPI network was calculated. The significant targets of the A. Excelsa-Obesity PPI network were obtained based on DC, BC, CC, EC, IC, LAC, NC, and SC. Finally, important targets were obtained, namely, Interleukin-6 (IL6), Tumor necrosis factor (TNF), RAC-alpha serine/threonine-protein kinase (AKT1), Vascular endothelial growth factor A (VEGFA), Serum albumin (ALB), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Catenin beta-1(CTNNB1), Epidermal growth factor receptor (EGFR), Interleukin-1 beta (IL-1B), Peroxisome proliferator-activated receptor gamma (PPARG), Signal transducer and activator of transcription 3 (STAT3), Estrogen receptor (ESR1), Hypoxia-inducible factor 1-alpha (HIF1A), NAD-dependent protein deacetylase sirtuin-1 (SIRT1), Serine/threonine-protein kinase mTOR (MTOR), Toll-like receptor 4 (TLR4), Peroxisome proliferator-activated receptor alpha (PPARA), Adiponectin (ADIPOQ), Receptor tyrosine-protein kinase erbB-2 (ERBB2) and Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) (Fig. [113]5). Fig. 5. [114]Fig. 5 [115]Open in a new tab (a) Ailanthus excelsa Roxb-Obesity PPI network, (b) PPI network by the screening criteria of DC ≥ 38, BC ≥ 1248.6538, CC ≥ 0.2555332, EC ≥ 0.04289, IC ≥ 9.871477, LAC ≥ 11.105263, NC ≥ 18.84516, and SC ≥ 1.0275286E21. (c)Ailanthus excelsa Roxb-Obesity PPI network by the screening criteria of DC ≥ 79, BC ≥ 1061.192, CC ≥ 0.266806, EC ≥ 0.11179, IC ≥ 11.329657, LAC ≥ 29.544, NC ≥ 54.41227, and SC ≥ 6.97917E21. The size and color shading of the nodes were ordered by degree. The thickness and color shading of the edges were set according to the degree of interaction between the nodes. MCODE cluster analysis of PPI network In order to further analyse the 255 common targets of A. excelsa and Obesity, find the key sub-networks, and speculate the main targets, the AE-Obesity PPI network was further computationally analyzed by MCODE. The PPI network was divided into 7 clusters (Figs. [116]6a–g). The score of clusters 1 (score = 22.82) was far higher than the other clusters. The degree of the targets in cluster 1 was higher, such as IL6 (degree = 98), TNF (degree = 93), AKT1 (degree = 88), VEGFA (degree = 88), IL1B (degree = 81), PTGS2 (degree = 78), PPARG (degree = 78). Fig. 6. [117]Fig. 6 [118]Open in a new tab Cluster analysis of Ailanthus excelsa Roxb-Obesity PPI Network (a) Cluster 1, Composed of 30 nodes and 231 edges (Score = 22.828) (b) Cluster 2, composed of 39 nodes and 281 edges (Score = 14.789). (c) Cluster 3, composed of 28 nodes and 105 edges (Score = 7.778). (d) Cluster 4, composed of 7 nodes and 14 edges (Score = 4.667). (e) Cluster 5, composed of 6 nodes and 9 edges (Score = 3.600). (f) Cluster 6, composed of 6 nodes and 8 edges (Score = 3.200). (G) Cluster 7, composed of 3 nodes and 3 edges (Score = 3.00). GO and KEGG pathway enrichment analyses of PPI network Enrichment analysis of the A. excelsa -Obesity PPI network was obtained. In GO enrichment analysis, 255 AE-Obesity common targets were highly enriched in 2027 biological processes (BP), 101 cellular fractions (CC), and 187 molecular functions (MF) by setting p-values less than 0.05. The top 20 significant results for each were taken as shown in the Fig. [119]7. Biological processes (BP) show a strong correlation with responses to oxygen-containing compounds, organic substances, chemicals, endogenous stimuli, organic cyclic compounds, hormones, and lipids. These responses, both general and cell-specific, are crucial for managing obesity. Additionally, regulatory mechanisms such as the regulation of biological quality, multicellular organismal processes, and cell communication play significant roles. Obesity influences these responses through external stimuli like diet and environment. The positive regulation of biological processes suggests mechanisms that enhance biological activity, which may be crucial for understanding the body’s adaptation to fat accumulation. This indicates a potential role for A. excelsa in obesity management. Fig. 7. [120]Fig. 7 [121]Open in a new tab Gene ontology analysis of PPI network (BP: Biological process, CC: Cellular component, MF: Molecular function). Response to oxygen-containing compound (GO:1901700) score the lowest false discovery rate of 6.75E-84 via the modulation of 145 genes i.e. CFTR, OTC, DRD4, CPB2, SIRT1, HMOX1, TIMP1, CTSH, PON1, SERPINE1, GAA, RPS6KB1, CCL2, CD38, NFKB1, IL2, CYP27B1, NR3C1, IGFBP2, GHSR, AHR, CD68, KCNA5, SLC6A4, IL1B, PIK3CA, BCHE, STAT3, DNMT3A, GCKR, CPT1A, GAL, SOD1, SLC6A3,REN, SRD5A1,EGFR, HTR2C, CA3,PPARG, ACE, CCR5,HMGB2,IL15,NOS3,MMP3,ACHE, BCR, INSR, ADRB2,DRD5,CXCL8,OGG1,GLUL, PRKACA, PPARD, GH1,HNF4A, EDNRA, HSD11B2,ROCK2,NQO1,EZH2,SLC2A4,HSPA5,PRKCD, CD86,MAPT, HRH3,ESR2,PDE4D, PRKAA1,FYN, C5AR1,ANO1,RET, HP, ARG1,PDE3A, RXRG, CES1,NTRK3,MTOR, DRD2,PARP1,PTGS2,BGLAP, CNR1,SCD, PTPN1,MMP9,ABL1,TLR4,CNR2,RXRB, AR, ABCA1,F7,WT1,FOXO1,AKR1C3,JAK2,DRD3,TFRC, G6PD, DRD1,CYP19A1,NFE2L2,BCL2,CRHR1,ROCK1,PPARA, IL6,ADIPOQ, TNF, ESR1,GLRA1,CD36,SLC2A1,PIK3CG, RXRA, AMY2A, IDO1,TYK2,JAK3,CASP1,HTR2A, HIF1A, TSHR, NR1H4,DIO2,AKT1,TRPV1,H6PD, CCL5,NR1H3,NOS1,CYP1B1,ACACA, CTNNB1,PRKCB, IGF1R, ENPP1,CALM1,and JAK1against 1547 background gene at a strength of 0.86. Cellular components (CCs) are closely correlated with membrane rafts, receptor complexes, plasma membrane components, vesicles, cytoplasm, cell periphery, and extracellular space. Membrane rafts and receptor complexes in the plasma membrane are critical for signaling pathways that regulate appetite and energy homeostasis. The integral and intrinsic components of the plasma membrane, along with vesicles, are essential for nutrient uptake, signal transduction, and lipid/glucose transport. Cytoplasm and cell periphery drive metabolic reactions, while extracellular signaling molecules influence cellular behavior. The endomembrane system, including mitochondria, is vital for protein and lipid processing in energy metabolism. The cell surface mediates interactions with the extracellular environment, impacting nutrient absorption and communication. Neural components such as the somatodendritic compartment regulate appetite and energy expenditure, underscoring the complex interplay in obesity regulation. Membrane raft (GO: 0045121) has the lowest false discovery rate (8.20E-17) via modulation of 34 genes (HMOX1, SLC6A2, GHSR, KCNA5, SLC6A4, NPC1, SLC6A3, EGFR, NOS3, INSR, S1PR1, PRKACA, SLC2A4, TRPM8, MAPT, FYN, ANO1, RET, DPP4, PTGS2, CNR1, ABCA1, JAK2, TNF, CD36, SLC2A1, HTR2A, LCK, NOS1, HK1, CTNNB1, ITGAM, IGF1R, ABCG2) against 320 background genes, with a strength of 0.91. MF was associated with Protein binding, Binding, Identical protein binding, signaling receptor activity, nuclear receptor activity, Ion binding and signaling receptor binding etc., the obtained molecular functions that are significant in the context of obesity, describing how different proteins and molecules interact and participate in cellular processes. Protein binding and identical protein binding refer to the interactions between proteins, which can affect signaling pathways and metabolic processes. Signaling receptor activity and signaling receptor binding are crucial as they relate to how cells receive and respond to external signals, which can influence appetite, energy expenditure, and fat storage. Nuclear receptor activity, including nuclear steroid receptor activity, involves receptors that regulate gene expression in response to hormones, impacting metabolism and fat distribution. Ion binding, such as cation and transition metal ion binding, affects enzyme function and cellular signaling. Catalytic activity, enzyme binding, and protein tyrosine kinase activity are involved in biochemical reactions and signal transduction pathways that regulate metabolism. Organic cyclic compound binding and small molecule binding relate to how the body processes various compounds, including drugs and hormones. Phosphotransferase activity, including kinase and protein kinase activities, involves phosphorylation processes critical for regulating metabolic pathways. Transferase activity, transferring phosphorus-containing groups, is essential for modifying proteins and metabolites, impacting energy metabolism. Understanding these molecular functions helps in deciphering the complex biological processes that contribute to obesity. In addition, a total of 202 pathways were enriched by KEGG enrichment analysis, and the obesity related important pathways and its connectiveness with targets, gene ratio, and its gene count were shown in the Fig. [122]8. The results indicated that A. excelsa may regulate Obesity through Adipocytokine signaling pathway, PPAR signaling pathway, Insulin signaling pathway as well as through Fatty acid biosynthesis, Fat digestion and absorption and Glycolysis / Gluconeogenesis. A. excelsa also regulates metabolism pathways such as the Galactose metabolism, Fructose and mannose metabolism, Cholesterol metabolism, Fatty acid metabolism, Starch and sucrose metabolism and metabolic pathways. Fig. 8. [123]Fig. 8 [124]Open in a new tab Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of Ailanthus excelsa. GO and KEGG pathway enrichment analyses of cluster 1 GO and KEGG enrichment analysis was performed on cluster 1 (score = 22.828), which had the highest score in the cluster analysis, to further obtain the functional information and pathway information of cluster 1. GO enrichment analysis was performed on cluster 1 by using ClueGO and CluePedia plugins. 30 targets present in cluster 1 were highly enriched in 227 biological processes by setting p-values less than 0.05. The significant results for each were taken as shown in the Fig. [125]9. GO:0001516 (prostaglandin biosynthetic process) involves genes like IL1B, PTGS2, and SIRT1, which are pivotal in inflammation and metabolic regulation. GO:0001935 (endothelial cell proliferation) and GO:0001937 (negative regulation of endothelial cell proliferation) highlight the role of genes such as CCL2, PPARG, and TNF in modulating vascular health and inflammation. GO:0002237 (response to molecule of bacterial origin) involves a range of immune response genes (e.g., IL1B, TNF, TLR4) crucial for managing systemic inflammation. GO:0002367 (cytokine production involved in immune response) and GO:0002526 (acute inflammatory response) emphasize the importance of cytokines like IL1B and TNF in inflammation. GO:0010874 and GO:0010875 (regulation of cholesterol efflux) show the role of APOA1, PPARG, and SIRT1 in lipid metabolism. GO:0010883 and GO:0010888 (regulation of lipid storage) and GO:0032368 (regulation of lipid transport) further highlight the involvement of PPARG and SIRT1 in managing lipid levels. Collectively, these genes and their associated processes are critical in controlling inflammation, lipid metabolism, and vascular health, all of which are essential for effective obesity management. Fig. 9. [126]Fig. 9 [127]Open in a new tab Cluster 1 Biological process (a) ClueGO analysis of biological process (b) CluePedia analysis of biological process. Furthermore, a total of 30 pathways were enriched by KEGG enrichment analysis, and the pathways were shown in the Fig. [128]10. In treating obesity, various KEGG pathways play crucial roles in modulating metabolic and inflammatory responses. The PPAR signaling pathway (KEGG:03320), involving genes such as APOA1, MMP1, PPARA, and PPARG, regulates lipid metabolism and enhances fat oxidation. The NF-kappa B signaling pathway (KEGG:04064), with genes like CXCL8, IL1B, PTGS2, TLR4, and TNF, controls inflammation, which is often elevated in obesity. Similarly, the HIF-1 signaling pathway (KEGG:04066) and the Toll-like receptor signaling pathway (KEGG:04620) involve genes such as HMOX1, IL6, TLR4, and TNF, which impact metabolic adaptations and inflammatory responses. The Adipocytokine signaling pathway (KEGG:04920) and Insulin resistance pathway (KEGG:04931), featuring PPARA, SLC2A1, and TNF, improve insulin sensitivity and glucose homeostasis, critical in obesity management. Additionally, pathways like the AGE-RAGE signaling pathway (KEGG:04933) and lipid and atherosclerosis (KEGG:05417) address oxidative stress and cardiovascular risks associated with obesity. By targeting these pathways, it is possible to balance energy metabolism, reduce inflammation, and improve insulin sensitivity, offering a comprehensive approach to obesity treatment. The bar graph and pie chart of biological process of cluster 1 given in supplementary Fig. S3, S4. [GO and KEGG pathway enrichment analyses of the cluster 2 and 3 given in supplementary file fig. S5-S8]. Fig. 10. [129]Fig. 10 [130]Open in a new tab Cluster 1 KEGG pathway analysis (a) ClueGO analysis (b) CluePedia analysis (c) Pie chart representation (d) Bar graph of KEGG pathways. Network construction and analysis The network analysis revealed potential relationships between compounds and targets, implying the pharmacological mechanisms of the compounds. Nodes with the highest degree of connections represent hubs in the network, indicating potential drugs or targets. The core component-target (C-T) network of A. excelsa for obesity was analyzed based on degree values. Apigenin emerged as a highly modulated component, with a degree of 40, eccentricity of 5, neighbourhood connectivity of 3.22, radiality of 0.9652, stress of 35,312, and a topological coefficient of 0.1392. Alongside Apigenin, 3-hydroxyphenylvaleric acid (degree = 10), selinidin (degree = 9), and quinic acid (degree = 7) also demonstrated significant modulation within the C-T network. These findings suggest that a single compound can target multiple receptors, contributing to the network’s interconnectedness. These compounds targeted key modulators of obesity, such as HK1, HK2, and ADIPOQ, as well as other targets involved in obesity-related complications, including PPARA and INSR. Furthermore, several targets, such as FASN, PIK3CA, MTOR, and AKT1, were synergistically regulated by different compounds, emphasizing the multitargeting nature of obesity treatment. The top 15 significant targets identified were HK1, HK2, PIK3CA, AKT1, AMY2A, GAA, MTOR, CD36, ACACB, SLC2A4, CPT1A, INSR, ACACA, FASN, and ADIPOQ. Pathway analysis, crucial in systems pharmacology, bridges receptor-ligand interactions with pharmacodynamics outcomes. To focus on disease relevance, obesity-associated pathways were used to construct the target-pathway (T-P) network. Using integrated KEGG pathway analysis, 238 interactions between 127 targets and 19 disease-associated pathways were mapped into the T-P network using Cytoscape 3.10.1 (P < 0.01). The T-P network identified metabolic pathways as the most modulated pathway (degree = 51, average shortest path length = 2.16, betweenness centrality = 0.45344, closeness centrality = 0.4629, eccentricity = 5, neighbourhood connectivity = 3.01961, radiality = 0.97725, stress = 100,380, and topological coefficient = 0.0594), followed by insulin resistance (degree = 26), AMPK signaling (degree = 24), JAK-STAT signaling (degree = 20), and insulin signaling pathways (degree = 19). The roles of these high-degree pathways in obesity are well-established. Additionally, other signaling pathways, such as the Adipocytokine signaling pathway and PPAR signaling pathway, also contribute to the development of obesity. An example of the synergism of compounds acting on metabolism pathways includes Fatty acid metabolism, Galactose metabolism, Fructose and mannose metabolism, Cholesterol metabolism, and Carbohydrate digestion and absorption (Fig. [131]11). In addition to disease-associated pathways, the compounds also influence non-disease-associated pathways, including the AGE-RAGE signaling pathway in diabetic complications (hsa04933), PI3K-Akt signaling pathway (hsa04151), Glucagon signaling pathway (hsa04922), and Non-alcoholic fatty liver disease (hsa04932). Since obesity can potentially develop into diabetes mellitus, it can be inferred that components present in A. excelsa could also prevent the development of diabetes mellitus. Detailed pathway information, including KEGG IDs, observed gene counts, background gene counts, false discovery rates, and matching proteins, is provided in Table S5. Fig. 11. [132]Fig. 11 [133]Open in a new tab Network analysis of Phytoconstituents present in Ailanthus excelsa and obesity related targets, pathways. One of the most significant pathways for A. excelsa in treating obesity, according to the degree value, is the metabolic pathways, indicating that A. excelsa may facilitate enzymatic reactions within cells that convert substrates into various end products. These pathways support energy production, biosynthesis of essential molecules, and waste elimination. Enzymes catalyse each step, ensuring efficient and regulated transformation of molecules, supporting vital cellular functions, and maintaining homeostasis in the body. By considering targets and pathways, A. excelsa could exert its therapeutic effects through influencing multiple pathways and acting on multiple targets in each pathway. Probable molecular mechanism modulated by Ailanthus excelsa components Genes involved in the treatment of obesity impact various metabolic pathways and processes. Activation genes include SIRT1, which enhances insulin sensitivity through protein deacetylation; PPARGC1A, which boosts mitochondrial function and oxidative metabolism; CPT1A, which facilitates fatty acid oxidation; FABP4, which aids fatty acid transport; and ADIPOQ, which improves insulin sensitivity and fatty acid metabolism. PPARG regulates adipocyte differentiation and lipid metabolism, while ACLY is crucial for fatty acid and cholesterol biosynthesis. FOXO1 and STAT3 play roles in gluconeogenesis and energy balance, respectively, and PRKACA activates protein kinase A, influencing glucose metabolism and lipolysis. In contrast, Inhibition genes such as FASN and ACACA promote lipid accumulation when overactive, while SCD modulates fat accumulation through fatty acid conversion. MTOR and NFKB1 are associated with metabolic disorders and inflammation linked to obesity, and PTGS2 contributes to obesity-related inflammation. Association genes like PIK3CA and INSR are involved in insulin signaling and glucose uptake, with dysregulation linked to obesity. CD36 influences fatty acid storage, and IL6 and HMGCS1 are associated with inflammation and metabolic regulation. RXRA and JAK2 are involved in lipid metabolism and cytokine signaling, respectively, while ADIPOQ is crucial for insulin sensitivity and obesity risk (Fig. [134]12). These genes collectively influence energy metabolism, fat storage, inflammation, and insulin sensitivity, highlighting their roles in obesity treatment ([36, 37]). Fig. 12. [135]Fig. 12 [136]Open in a new tab Probable molecular mechanism of Ailanthus excelsa Roxb components and its targeted proteins in AMPK signalling pathway (KEGG ID: map04152). Molecular docking Molecular docking studies on α-amylase and α-glucosidase Among the selected phytocompounds from the literature, compound Isoquercitrin demonstrating highest binding affinity at − 8.96 and glide energy − 55.83 kcal/mol and displayed similar bond interactions as opposed to standard acarbose with ASP197, GLU233, ILE235, ASP300 (Fig. [137]14a). and Acarbose displays binding affinity at -10.36 and glide energy − 54.0 kcal/mol and displays hydrogen bond interaction with ASP197, GLU233, ILE235, ASP300, ARG195, LYS200, GLU240, TYR151 residues in α-amylase protein (PDB ID:4W93 / Fig. [138]13a). Similarly, in α-glucosidase binding pocket (PDB ID: 3A47). Isoquercitrin demonstrating highest binding affinity at -10.41 and glide energy − 59.44 kcal/mol and displayed similar bond interactions as opposed to standard acarbose with PRO309, GLU304, ASP408 (Fig. [139]13b) and Vitexin demonstrating second highest binding affinity at − 10.21 and glide energy − 52.75 kcal/mol with SER308, PHE157, LYS155, HIE239 and Acarbose displays binding affinity at -10.2 and glide energy − 62.38 kcal/mol and displays hydrogen bond interaction with PRO309, ASN241, GLU304, ASP408, PHE157 residues (Fig. [140]14b). Fig. 14. [141]Fig. 14 [142]Open in a new tab Standard Acarbose in (a) α-amylase protein with ASP197, GLU233, ILE235, ASP300, ARG195, LYS200, GLU240, TYR151 (PDB ID:4W93) (b) α-glucosidase binding pocket with PRO309, ASN241, GLU304, ASP408, PHE157 amino acid residues (PDB ID:3A47). Fig. 13. [143]Fig. 13 [144]Open in a new tab Isoquercitrin in (a) α-amylase protein with ASP197, GLU233, ILE235, ASP300 residues (PDB ID: 4W93) (b) α-glucosidase binding pocket with SER308, PHE157, LYS155, HIE239 (PDB ID: 3A47). Molecular docking studies on lipase and HMG-CoA Similarly, in Lipase (PDB ID: ILPB) binding pocket compound Isoquercitrin demonstrating highest binding affinity at -9.96 and glide energy − 52.84 kcal/mol and displayed bond interactions with ARG44, LEU41, ARG337, ASP331, ALA332, GLN29 and standard Orlistat displayed − 2.8 and glide energy − 43.12 kcal/mol and interactions with ARG44, LEU41 and ARG337 Fig. [145]15. Fig. 15. [146]Fig. 15 [147]Open in a new tab 2D Orientation of (a) Isoquercitrin with ARG44, LEU41, ARG337, ASP331, ALA332, GLN29 residues (b) Standard orlistat with ARG44, LEU41 and ARG337 residues in lipase binding pocket (PDB ID: 1LPB). Figure. 16. shows the binding interactions of Isoquercitrin and simvastatin within the HMG-CoA binding pocket (PDB ID: 1HW9). Isoquercitrin exhibits a binding affinity of − 7.11 and a glide energy of − 37.60 kcal/mol. Its interactions include key residues such as ALA751, LYS735, GLU559, and GLY560. In contrast, the standard drug simvastatin demonstrates a lower binding affinity of -2.13 and a glide energy of -26.82 kcal/mol. Simvastatin interacts primarily with GLU559 and ASN755, forming a salt bridge with LYS735 (Fig. [148]16). Fig. 16. [149]Fig. 16 [150]Open in a new tab 2D Orientation of (a) Isoquercitrin with ALA751, LYS735, GLU559, GLY560 residues, (b) Standard simvastatin with GLU559, ASN755 and salt bridge with LYS735 residues in HMG-CoA binding pocket (PDB ID: 1HW9). Molecular dynamics simulation study A molecular dynamics simulation was conducted to investigate the stability and conformational changes of specific Isoquercitrin within the binding pocket of lipase (PDB ID: 1LPB) and HMG-CoA protein (PDB ID: 1HW9). The Desmond program was utilized to analyze interactions during the 100ns simulation, with key properties such as Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and hydrogen bond contacts being assessed. The RMSD values reflect alterations in both protein and ligand conformations relative to the initial reference structure (Frame 0) chosen for the simulation. Compound Isoquercitrin was analysed by Protein-ligand RMSD plot. Protein structure RMSD to reference C-alpha RMSD and Backbone RMSD value showed a maximum deviation of 2.169 Ǻ and 2.186 Ǻ (frame 125) respectively. Ligand stability was assessed by ligand RMSD to Ligand aligned on protein and ligand aligned on ligand indicating a maximum deviation of 2.481 Ǻ and 1.478 Ǻ (Frame 147) in Lipase protein. The Protein RMSF plot of Isoquercitrin showed ASP_249 showed maximum fluctuation of 2.142 Ǻ and 1.943 (frame 337) for C-alpha and protein backbone RMSF. The Ligand RMSF plot showed high fluctuation with RMSF values of 2.220 Ǻ and 1.389 Ǻ (frame 23) aligned on protein and aligned on ligand respectively (Fig. [151]17). Fig. 17. [152]Fig. 17 [153]Open in a new tab (a) Protein Ligand RMSD Plot of Isoquercitrin, (b) Protein RMSF Plot, (c) Protein Ligand Contacts timeline, (d) Ligand RMSF plot over period of 100 ns within lipase protein. Compound Isoquercitrin was analysed by Protein-ligand RMSD plot. Protein structure RMSD to reference C-alpha RMSD and Backbone RMSD value showed a maximum deviation of 2.671 Ǻ and 2.687 Ǻ (frame 228) respectively. Ligand stability was assessed by ligand RMSD to Ligand aligned on protein and ligand aligned on ligand indicating a maximum deviation of 2.456 Ǻ and 2.246 Ǻ (Frame 53) in HMG-CoA protein. The Protein RMSF plot of Isoquercitrin showed LYS735 showed maximum fluctuation of 2.606 Ǻ and 2.633 (frame 294) for C-alpha and protein backbone RMSF. The Ligand RMSF plot showed high fluctuation with RMSF values of 4.653 Ǻ and 0.670 Ǻ (frame 14) aligned on protein and aligned on ligand respectively (Fig. [154]18). Fig. 18. [155]Fig. 18 [156]Open in a new tab (a) Protein Ligand RMSD Plot of Isoquercitrin, (b) Protein RMSF Plot, (c) Protein Ligand Contacts timeline, (d) Ligand RMSF plot over period of 100 ns within HMG-CoA protein. Intermolecular contacts in molecular dynamics simulation The stacked bar chart in Fig. [157]19. Presents a stacked bar chart depicting intermolecular contacts between inhibitors and the protein observed throughout the molecular dynamic’s simulation. This visualization categorizes interactions into distinct types, including hydrogen bonds, hydrophobic interactions, ionic interactions, and water bridges. Each interaction type is further subdivided to provide detailed insights into the nature of the interactions occurring during the simulation. The simulation interaction diagram explores these interactions, and Isoquercitrin is identified as the best-scoring inhibitor, with H-bonds and water bridges with SER35, LEU36, ARG38, LEU41, LYS239, ASP247, ILE248. Hydrophobic interactions are observed with ASP332 and the 2D interaction of Isoquercitrin has a polar interaction with GLN29, water bridge with LEU41, ASP389, GLU13, and charged (negative) bond with ASP331, ASP247, ASP31 amino acids in lipase pocket in lipase protein and Similarly, Isoquercitrin is identified as the best-scoring inhibitor, with H-bonds and water bridges with GLU559, GLY560, ARG568, LEU721, ASN755, GLY849 and the 2D interaction of Isoquercitrin has charged (negative) bond with GLU559 and water bridge with GLY849 amino acids in HMG-CoA protein. Fig. 19. [158]Fig. 19 [159]Open in a new tab (a) Protein ligand contacts of compound Isoquercitrin with the respective amino acids of the lipase protein (b) Ligand protein contacts of Isoquercitrin with the respective amino acids of the HMG-CoA protein. Discussion The present study was designed to investigate the interaction of bioactives from A. Excelsa with proteins involved in obesity and diabetes, and further propose the molecular mechanism of A. Excelsa in the management of metabolic dysfunction like obesity and diabetes via integrating various computational chemistry, system biology tools like molecular dynamic simulations, gene enrichment analysis, gene ontology, and cluster analysis with experimental in vitro results. Initially, the phytochemical analysis of the three fractions, which include hydro alcoholic, ethyl acetate, and N-hexane fractions, was subjected to estimate the total phenol, flavonoid, and tannin content, among which ethyl acetate was found to possess a high content of flavonoids and alkaloids. Further the phytoconstituent, from all the extract were retrieved from Dr. Dukes, IMPPAT and literature search, we identified macromolecule targets involved in pathogenesis of obesity and diabetes. Hence alteration in the molecular function of these identified protein targets can be possible by binding of the bioactive molecules. Hence it becomes the rationale behind the usage of phytochemicals of A. Excelsa in treatment of metabolic dysfunction like obesity and diabetes. Adiponectin (ADIPOQ) produced by the adipocytes, is one of the highly modulated protein by the bioactives of A. Excelsa and is associated with obesity and insulin resistance^[160]37. In obesity adiponectin levels are decreased^[161]38, the cholesterol accumulation in adipose tissue dysregulates adipocyte functions, owing to reduced adiponectin secretion^[162]39. Also, the dysregulation of the mevalonate pathway which occurs via the HMG-CoA reductase enzyme causes to inflammation and oxidative stress, which leads to suppressing of adiponectin levels^[163]40,[164]41. Thus, the molecules which inhibit the HMG-CoA reductase enzyme have shown to increase adiponectin levels previous studies^[165]42. Hence in present study, the three extract were screened for their inhibitory potential against the, HMG-CoA enzyme inhibition. Among them, Ethyl acetate extract was found to be the better inhibitor of the HMG-CoA. Also, the molecular docking studies revealed the binding of phytoconstituent in the binding pocket of HMG-CoA enzyme. Isoquercetin showed highest binding interaction with the binding Glide energy of -37 kcal/mol with three hydrogen bond interaction with ALA 751, GLU 559, and GLY 560 as compared to standard simvastatin. The MD simulation results revealed there was fluctuation seen in the protein ligand RMSD of Isoquercetin-HMG-CoA reductase complex, which was stabilized after the 85ns. However, the, RMSF was less than 3Å with the amino acid residues in contact with the ligand, owing to its better binding throughout the simulation. Similarly, there exist a close association of adiponectin and lipase activity, as adiponectin levels are inversely related to lipase activity, increase in the lipase activity cause enhanced fat absorption and storage leading to adiposity which further cause in reduction of adiponectin levels^[166]43,[167]44. Thus, reduced adiponectin level in obesity cause impaired lipid metabolism and insulin sensitivity. Hence targeting the pancreatic lipase enzyme can help increase the adiponectin levels leading to better lipid metabolism^[168]45,[169]46. Molecular docking at the lipase target, displayed Isoquercetin as better binding bioactive with the binding glide energy of -52.84 kcal/mol with five hydrogen bond interactions with LEU 41, ARG 337, ASP 331, ALA 332, and GLN 29, as compared to standard orlistat. The RMSD analysis of isoquercetin-lipase enzyme displayed better stability with deviation of less than 3Å. Also, the RMSF was seen to be fluctuating between 1Å and 2Å indicating stable complex throughout the simulation. Postprandial hyperglycemia is strongly associated with the progression of obesity and metabolic disorders, α-amylase and α-glucosidase are the two main enzymes involved in the breakdown polysaccharides into glucose, which cause surge in blood glucose levels in diabetic condition which leads to fat accumulation and lipogenesis, which causes the suppression of adiponectin levels, which ultimately leads to increased fat storage and expansion of adipose tissue^[170]47. Herein the molecular docking results displayed Isoquercetin to be the highest docked bioactive against the α-amylase enzyme with the glide binding energy of -55.83 kcal/mol with hydrogen bond interactions with ASP 197, GLU 233, ILE 235, and ASP 300. Isoquercetin showed glide binding energy of -59.44 kcal/mol and hydrogen bonding with PRO 309, GLU 304, and ASP 408 residues as compared to standard acarbose. Moreover, it is important to recognize that a single compound has the potential to interact with multiple proteins via modulating multiple pathways^[171]48. The current study further emphasizes the evaluation of other lead compounds derived from A. Excelsa to explore their potential for modulating multiple pathways involved in the pathogenesis of obesity and validating the other protein targets interacting with the bioactives. Conclusion This study represents the first comprehensive evaluation of the antioxidant and enzyme inhibitory activities of Ailanthus excelsa, incorporating cluster analysis to further elucidate its effects. Our findings provide compelling evidence of the plant’s therapeutic potential for managing obesity through the modulation of key metabolic enzymes. Network pharmacology analysis identified critical targets associated with obesity, including ADIPOQ, PPARA, PPARG, IL6, TNF, and AKT1, which are involved in modulating metabolic pathways. Isoquercetin demonstrated strong binding affinities to HMG-CoA reductase, lipase, α-amylase, and α-glucosidase, supporting its role as a bioactive metabolite in the plant’s anti-obesity effects. The ethyl acetate fractions exhibited potent inhibitory activities, with IC[50] values of 56.25 ± 4.85 µg/mL for lipase, 108.27 ± 3.38 µg/mL for HMG-CoA reductase, 117.08 ± 3.28 µg/mL for α-glucosidase, and 125.93 ± 2.29 µg/mL for α-amylase. Future studies should focus on isolating and characterizing the individual bioactive compounds within the plant to better understand their structural and functional attributes. Furthermore, the promising results from this study pave the way for exploring the antidiabetic and anti-obesity properties of A. excelsa in greater detail. Continued investigation into its bioactive components and their interactions with metabolic pathways will provide valuable insights for the development of novel therapeutic strategies for obesity and related metabolic disorders. Supplementary Information Below is the link to the electronic supplementary material. [172]Supplementary Material 1^ (3.4MB, docx) Acknowledgements