In Silico Evaluation of Kaempferol, Gallic Acid, and Stigmasterol from Lagerstroemia speciosa as Multi-Target Antidiabetic Agents: Molecular Docking and Dynamics Simulation Study
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Submitted
30 April 2025
Published
30 June 2026
Keywords:
-
Antidiabetic, Lagerstroemia speciosa, Kaempferol, Molecular dynamics
Abstract
Diabetes mellitus (DM) is a chronic metabolic disorder that leads to severe complications and continues to increase in prevalence worldwide. Although Lagerstroemia speciosa is a well-recognized antidiabetic medicinal plant, most in silico studies have focused exclusively on its major constituent, leaving the antidiabetic potential of its other phytochemicals largely unexplored. This study investigated the multi-target antidiabetic potential of phytochemicals derived from L. speciosa leaves using an in silico approach targeting three key enzymes: aldose reductase, glucokinase, and glycogen synthase kinase 3-beta (GSK3-β). A total of 62 compounds were screened by molecular docking with AutoDock Vina, followed by toxicity predictions using ProTox-II and ToxTree. The top ligand for each target, kaempferol (aldose reductase), gallic acid (glucokinase), and stigmasterol (GSK3-β), was selected for further evaluation through molecular dynamics simulations using GROMACS 2016.3 for 100 ns. Structural and interaction stability were assessed through RMSD, RMSF, SASA, Rg, and RDF analyses. Binding free energies were calculated using the MM/PBSA method via g_mmpbsa. The results indicated that stigmasterol exhibited the most favorable MM/PBSA binding free energy (–133.377 kJ/mol), followed by kaempferol (–65.714 kJ/mol) and gallic acid (–45.629 kJ/mol). However, this favorable energy was dominated by nonspecific van der Waals contributions, consistent with the diffuse interaction patterns and low hydrogen-bond occupancy (4.24%) for stigmasterol. Kaempferol exhibited the highest hydrogen-bond occupancy (64.38%), indicating a stable, consistent interaction with its target enzyme. Rg and RDF analyses confirmed the compactness and specific atomic interactions of the kaempferol and gallic acid complexes.
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References
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2. Adnan Y, Hadju V, Mallongi A, Ali MSS. The Economic Cost of Type 2 Diabetes in Indonesia: A Systematic Review. Iran J Public Health. 2025;54(10):2139-50. DOI: 10.18502/ijph.v54i10.20118; PMID: 41357699; PMCID: PMC12675950.
3. Ryszkiewicz P, Malinowska B, Schlicker E. Polypharmacology: new drugs in 2023-2024. Pharmacol Rep. 2025;77(3):543-60. DOI: 10.1007/s43440-025-00715-8; PMID: 40095348; PMCID: PMC12066383.
4. Polonsky WH, Henry RR. Poor medication adherence in type 2 diabetes: recognizing the scope of the problem and its key contributors. Patient Prefer Adherence. 2016;10:1299-307. DOI: 10.2147/PPA.S106821; PMID: 27524885; PMCID: PMC4966497.
5. Coimbra JTS, Feghali R, Ribeiro RP, Ramos MJ, Fernandes PA. The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer. RSC Adv. 2021;11(2):899-908. DOI: 10.1039/d0ra09995c; PMID: 35423709; PMCID: PMC8693363.
6. Lin A, Zhang Z, Jiang A, Li K, Shi Y, Yang H, et al. Computational approaches to druggable site identification: Current status and future perspective. Acta Pharm Sin B. 2026;16(1):62-92. DOI: 10.1016/j.apsb.2025.10.032; PMID: 41584329; PMCID: PMC12827903.
7. Arif R, Ahmad S, Mustafa G, Mahrosh HS, Ali M, Qamar MTU, et al. Molecular Docking and Simulation Studies of Antidiabetic Agents Devised from Hypoglycemic Polypeptide-P of Momordica charantia. Biomed Res Int. 2021;2021:5561129. DOI: 10.1155/2021/5561129; PMID: 34589547; PMCID: PMC8476269.
8. Singh M, Kapoor A, Bhatnagar A. Physiological and Pathological Roles of Aldose Reductase. Metabolites. 2021;11(10):655. DOI: 10.3390/metabo11100655; PMID: 34677370; PMCID: PMC8541668.
9. Aqel YA, Alnesf A, Aigha II, Islam Z, Kolatkar PR, Teo A, et al. Glucokinase (GCK) in diabetes: from molecular mechanisms to disease pathogenesis. Cell Mol Biol Lett. 2024;29(1):120. DOI: 10.1186/s11658-024-00640-3; PMID: 39245718; PMCID: PMC11382428.
10. Wang L, Li J, Di LJ. Glycogen synthesis and beyond, a comprehensive review of GSK3 as a key regulator of metabolic pathways and a therapeutic target for treating metabolic diseases. Med Res Rev. 2022;42(2):946-82. DOI: 10.1002/med.21867; PMID: 34729791; PMCID: PMC9298385.
11. Yue Z, Xu Y, Cai M, Fan X, Pan H, Zhang D, Zhang Q. Floral Elegance Meets Medicinal Marvels: Traditional Uses, Phytochemistry, and Pharmacology of the Genus Lagerstroemia L. Plants. 2024;13(21):3016. DOI: 10.3390/plants13213016; PMID: 39519935; PMCID: PMC11548200.
12. Sonar MP, Rathod VK. Extraction of type II antidiabetic compound corosolic acid from Lagerstroemia speciosa by batch extraction and three phase partitioning. Biocatal Agric Biotechnol. 2020;27:101694. DOI: 10.1016/j.bcab.2020.101694.
13. Sirikhansaeng P, Tanee T, Sudmoon R, Chaveerach A. Major Phytochemical as γ-Sitosterol Disclosing and Toxicity Testing in Lagerstroemia Species. Evid Based Complement Alternat Med. 2017;2017:7209851. DOI: 10.1155/2017/7209851; PMID: 28191023; PMCID: PMC5278189.
14. Yin B, Bi YM, Fan GJ, Xia YQ. Molecular Mechanism of the Effect of Huanglian Jiedu Decoction on Type 2 Diabetes Mellitus Based on Network Pharmacology and Molecular Docking. J Diabetes Res. 2020;2020:5273914. DOI: 10.1155/2020/5273914; PMID: 33134394; PMCID: PMC7593729.
15. Venkateswarulu TC, Vajiha, Krupanidhi S, Mikkili I, Angelina J, Babu DJ, et al. In silico study on evaluation of corosolic acid of Lagerstroemia speciosa against Alzheimer’s disease. Arab Gulf Journal of Scientific Research. 2023;41(2):175–82. DOI: 10.1108/AGJSR-04-2022-0039.
16. Chandran M, George S, Santhalingam K, Gangwar P, Krishnakumar K. Molecular docking Studies of 2α-Hydroxyursolic acid derivatives for hypercholesterolemia. Int J PharmTech Res. 2011;3(3):1576-81.
17. Choi JS, Ku PT, Cho KS, Huh MK. Comparison of Chemicals in Lagerstroemia speciosa (L.) Pers. at Growing Stage Levels by GC-MS. Korean J Crop Sci. 2010;55(3):200-6.
18. Al-Snafi AE. Medicinal Value of Lagerstroemia speciosa: An Updated Review. Int J Curr Pharm Res. 2019;11(5):18–26. DOI: 10.22159/ijcpr.2019v11i5.35708.
19. Pratama MRF, Praditapuspa EN, Kesuma D, Poerwono H, Widiandani T, Siswodihardjo S. Boesenbergia Pandurata as an Anti-Breast Cancer Agent: Molecular Docking and ADMET Study. Lett Drug Des Discov. 2022;19(7):606-26. DOI: 10.2174/1570180819666211220111245.
20. Wu K, Kwon SH, Zhou X, Fuller C, Wang X, Vadgama J, et al. Overcoming Challenges in Small-Molecule Drug Bioavailability: A Review of Key Factors and Approaches. Int J Mol Sci. 2024;25(23):13121. DOI: 10.3390/ijms252313121; PMID: 39684832; PMCID: PMC11642056.
21. EFSA Scientific Committee; More SJ, Bampidis V, Benford D, Bragard C, Halldorsson TI, et al. Guidance on the use of the Threshold of Toxicological Concern approach in food safety assessment. EFSA J. 2019;17(6):e05708. DOI: 10.2903/j.efsa.2019.5708; PMID: 32626331; PMCID: PMC7009090.
22. Kroes R, Renwick AG, Cheeseman M, Kleiner J, Mangelsdorf I, Piersma A, et al. Structure-based thresholds of toxicological concern (TTC): guidance for application to substances present at low levels in the diet. Food Chem Toxicol. 2004;42(1):65-83. DOI: 10.1016/j.fct.2003.08.006; PMID: 14630131.
23. Yamada T, Kurimoto M, Hirose A, Yang C, Rathman JF. Development of a New Threshold of Toxicological Concern Database of Non-cancer Toxicity Endpoints for Industrial Chemicals. Front Toxicol. 2021;3:626543. DOI: 10.3389/ftox.2021.626543; PMID: 35295111; PMCID: PMC8915903.
24. Jurowski K, Krośniak A. Prediction of key toxicity endpoints of AP-238 a new psychoactive substance for clinical toxicology and forensic purposes using in silico methods. Sci Rep. 2024;14(1):28977. DOI: 10.1038/s41598-024-79453-5; PMID: 39578526; PMCID: PMC11584713.
25. Shen T, Shen H, Kong Y, Qiang W, Yu X, Wang J. Structure-based virtual screening identifies novel small-molecule inhibitors targeting the endonuclease active site of APE1. Sci Rep. 2026;16(1):21299. DOI: 10.1038/s41598-026-51975-0; PMID: 42106528; PMCID: PMC13346695.
26. Xiong C, Kandhan P, Chen D, Ma Z, Smith ED, Tao P. Efficient Sampling of Short Protein Trajectories with Conditional Diffusion Models. J Chem Theory Comput. 2026;22(1):78-94. DOI: 10.1021/acs.jctc.5c01579; PMID: 41481844; PMCID: PMC12861079.
27. Makeneni S, Thieker DF, Woods RJ. Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking. J Chem Inf Model. 2018;58(3):605-14. DOI: 10.1021/acs.jcim.7b00588; PMID: 29431438; PMCID: PMC6067002.
28. Nettey-Oppong EE, Muhammad R, Ali A, Jeong HW, Seok YS, Kim SW, et al. The Impact of Temperature and Pressure on the Structural Stability of Solvated Solid-State Conformations of Bombyx mori Silk Fibroins: Insights from Molecular Dynamics Simulations. Materials. 2024;17(23):5686. DOI: 10.3390/ma17235686; PMID: 39685120; PMCID: PMC11642577.
29. Calderon A, Harbinson E, Ettrich R, Kulik N, Carey J. An MD View of Ligand Binding. Molecules. 2025;30(24):4678. DOI: 10.3390/molecules30244678; PMID: 41471704; PMCID: PMC12736043.
30. Cao X, Hummel MH, Wang Y, Simmerling C, Coutsias EA. Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs. J Chem Theory Comput. 2024;20(11):4456-68. DOI: 10.1021/acs.jctc.3c01366; PMID: 38780181; PMCID: PMC11530138.
31. Wang Y, Zhou Y, Khan FI. Molecular Insights into Structural Dynamics and Binding Interactions of Selected Inhibitors Targeting SARS-CoV-2 Main Protease. Int J Mol Sci. 2024;25(24):13482. DOI: 10.3390/ijms252413482; PMID: 39769245; PMCID: PMC11677904.
32. Tanner JJ. Empirical power laws for the radii of gyration of protein oligomers. Acta Crystallogr D Struct Biol. 2016;72(Pt 10):1119-29. DOI: 10.1107/S2059798316013218; PMID: 27710933; PMCID: PMC5053138.
33. Anand AA, Anwar S, Yadav V, Samanta SK. A comparative study of computational modeling approaches for evaluating structural dynamics and algorithmic suitability of short length peptides. Sci Rep. 2025;15(1):34351. DOI: 10.1038/s41598-025-16866-w; PMID: 41038912; PMCID: PMC12491430.
34. de Freitas RF, Schapira M. A systematic analysis of atomic protein-ligand interactions in the PDB. Medchemcomm. 2017;8(10):1970-81. DOI: 10.1039/c7md00381a; PMID: 29308120; PMCID: PMC5708362.
35. Goharshadi EK. A review on the radial distribution function: Insights into molecular structure, intermolecular interactions, and thermodynamic properties. J Mol Liq. 2025;433:127900. DOI: 10.1016/j.molliq.2025.127900.
36. Swiatla-Wojcik D. Simulation Studies of the Dynamics and the Connectivity Patterns of Hydrogen Bonds in Water from Ambient to Supercritical Conditions. Molecules. 2024;29(23):5513. DOI: 10.3390/molecules29235513; PMID: 39683673; PMCID: PMC11644018.
37. Bertalan É, Konno M, Marín MDC, Bagherzadeh R, Nagata T, Brown L, et al. Hydrogen-Bonding and Hydrophobic Interaction Networks as Structural Determinants of Microbial Rhodopsin Function. J Phys Chem B. 2024;128(30):7407-26. DOI: 10.1021/acs.jpcb.4c02946; PMID: 39024507.
38. Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci. 2018;4:87. DOI: 10.3389/fmolb.2017.00087; PMID: 29367919; PMCID: PMC5768160.
39. Yasir M, Park J, Han ET, Han JH, Park WS, Chun W. Investigating the Inhibitory Potential of Flavonoids against Aldose Reductase: Insights from Molecular Docking, Dynamics Simulations, and gmx_MMPBSA Analysis. Curr Issues Mol Biol. 2024;46(10):11503-18. DOI: 10.3390/cimb46100683; PMID: 39451563; PMCID: PMC11506312.
40. Quilantang NG, Limbo CA, Lee JS, Jacinto SD, Moon SK, Lee S. Aldose reductase inhibition of Rosa hybrida petals and its active component, kaempferol. Hortic Environ Biotechnol. 2020;61:601–7. DOI: 10.1007/s13580-020-00232-y.
Authors
1.
Putra AMP, Kurniawan CA, Sari AK, Akbar NH, Muslimawati K, Sari OM, Sandi DAD, Normaidah N, Buih PHJ, Haniffadli A. In Silico Evaluation of Kaempferol, Gallic Acid, and Stigmasterol from Lagerstroemia speciosa as Multi-Target Antidiabetic Agents: Molecular Docking and Dynamics Simulation Study. Borneo J Pharm [Internet]. 2026Jun.30 [cited 2026Sep.6];9(2):198-212. Available from: https://journal.umpr.ac.id/index.php/bjop/article/view/9720
Copyright (c) 2026 Aditya Maulana Perdana Putra, Catherina Adeline Kurniawan, Anna Khumaira Sari, Nabila Hadiah Akbar, Khoirunnisa Muslimawati, Okta Muthia Sari, Dita Ayulia Dwi Sandi, Normaidah Normaidah, Putri Helena Junjung Buih, Ariranur Haniffadli
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