Screening and Profiling of Bioactive Compounds from Moringa Oleifera Fruit Interaction with Advanced Glycation End Product Protein: A Molecular Docking Approach for Anti-Atherosclerosis Candidate Identification
Abstract
Diabetes mellitus represents a rapidly expanding worldwide health challenge, with estimates suggesting it will impact 643 million adults by 2030, with atherosclerosis representing a primary complication that substantially elevates disease burden and mortality rates. Chronic hyperglycemia compromises vascular equilibrium, resulting in endothelial impairment and atheromatous plaque development, potentially causing fatal thrombotic complications. Advanced glycation end products (AGEs) and their corresponding receptor RAGE are pivotal in diabetic vascular pathology, accelerating atherosclerotic development through both direct and indirect pathways. Moringa oleifera show potential as a natural therapeutic intervention with anti-glycation capabilities, although investigation of active constituents in M. oleifera fruit for RAGE protein inhibition remains insufficient. This study aimed to evaluate the capacity of bioactive compounds from the oleifera fruit to bind with the RAGE protein using computational analysis. The RAGE protein configuration (PDB ID: 3O3U) was retrieved from the RCSB database, while test compounds containing M. oleifera fruit metabolites were obtained from the Phytochem database. Molecular docking analysis was performed using PyRx software with AutoDock Vina. Drug-like characteristics were evaluated through SwissADME and pkCSM platforms, applying Lipinski's criteria. Protein-ligand visualization was performed using Biovia Discovery Studio and PyMol. This study revealed that nine bioactive compounds showed favourable RAGE protein binding with negative Gibbs free energy (-3.3 to -7.7 kcal/mol). Riboflavin demonstrated optimal binding affinity (-7.7 kcal/mol), followed by thiamine (-7.4 kcal/mol) and indole acetonitrile (-7.0 kcal/mol). These compounds established hydrogen bonds with 5-8 essential amino acid residues, resembling native ligand binding patterns. This study shows that riboflavin and thiamine exhibit strong RAGE protein binding affinity, representing promising therapeutic candidates for anti-atherosclerosis treatment targeting AGE-RAGE pathways in diabetic complications. Further studies should further validated using in-vitro, in-vivo, and clinic-based phase trials.
Keywords:
Atherosclerosis, Diabetes Complications, Molecular Docking, Moringa Oleifera Fruit, RAGE Protein
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References
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Al-Attas, O., Al-Daghri, N., Alokail, M., Abd-Alrahman, S., Vinodson, B., & Sabico, S. (2014). Metabolic benefits of six-month thiamine supplementation in patients with and without diabetes mellitus type 2. Clinical Medicine Insights: Endocrinology and Diabetes, 7, 1–6. https://doi.org/10.4137/CMED.S13573
Ameji, P. J., Uzairu, A., Shallangwa, G. A., & Uba, S. (2023). Molecular docking-based virtual screening, drug-likeness, and pharmacokinetic profiling of some anti-Salmonella typhimurium cephalosporin derivatives. Journal of Taibah University Medical Sciences, 18(6), 1417-1431. https://doi.org/10.1016/j.jtumed.2023.05.021
Auli, W. N., Husniati, H., Suprahman, N. Y., Fauziyya, R., Sarmoko, S., Ashari, A., ... & Fasya, G. A. (2024). Study of Gnetum gnemon metabolites as potential anti-breast and prostate cancer by metabolomic and molecular docking. Journal of Applied Pharmaceutical Science, 14(12), 120-130. https://dx.doi.org/10.7324/JAPS.2024.170723
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du Toit, E. S. (2019, November). Horticultural research review on Moringa oleifera trees growing in South Africa under sub-optimal conditions. In II International Symposium on Moringa 1306 (pp. 1-12). https://doi.org/10.17660/ActaHortic.2021.1306.1
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Gadaleta, D., Vuković, K., Toma, C., Lavado, G. J., Karmaus, A. L., Mansouri, K., ... & Roncaglioni, A. (2019). SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data. Journal of Cheminformatics, 11(1), 58. https://doi.org/10.1186/s13321-019-0383-2
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Guvatova, Z. G., Vakhrusheva, A., & Moskalev, A. (2025). A receptor for glycation end products (RAGE) is a key transmitter between garb-aging and inflammaging. Ageing Research Reviews, 113, 102919. https://doi.org/10.1016/j.arr.2025.102919
Indurthi, V. S., Jensen, J. L., Leclerc, E., Sinha, S., Colbert, C. L., & Vetter, S. W. (2020). The Trp triad within the V-domain of the receptor for advanced glycation end products modulates folding, stability and ligand binding. Bioscience Reports, 40(1), BSR20193360. https://doi.org/10.1042/BSR20193360
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2025). PubChem 2025 update. Nucleic Acids Research, 53(D1), D1516-D1525. https://doi.org/10.1093/nar/gkae1059
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Lang, S., Braz, N. F., Slater, M. J., & Kidley, N. J. (2025). In Silico Methods for Ranking Ligand–Protein Interactions and Predicting Binding Affinities: Which Method is Right for You? Journal of Medicinal Chemistry, 68(19), 19795-19799. https://doi.org/10.1021/acs.jmedchem.5c02582
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Madushanka, A., Moura Jr, R. T., Verma, N., & Kraka, E. (2023). Quantum mechanical assessment of protein–ligand hydrogen bond strength patterns: insights from semiempirical tight-binding and local vibrational mode theory. International Journal of Molecular Sciences, 24(7), 6311. https://doi.org/10.3390/ijms24076311
Majewski, M., Ruiz-Carmona, S., & Barril, X. (2019). An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Communications Chemistry, 2(1), 110. https://doi.org/10.1038/s42004-019-0205-5
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Nivatya, H. K., Singh, A., Kumar, N., Sonam, Sharma, L., Singh, V., ... & Mishra, A. K. (2025). Assessing molecular docking tools: understanding drug discovery and design. Future Journal of Pharmaceutical Sciences, 11(1), 111. https://doi.org/10.1186/s43094-025-00862-y
Pantsar, T., & Poso, A. (2018). Binding affinity via docking: fact and fiction. Molecules, 23(8), 1899. https://doi.org/10.3390/molecules23081899
Park, H., & Boyington, J. C. (2010). The 1.5 Å crystal structure of human receptor for advanced glycation endproducts (RAGE) ectodomains reveals unique features determining ligand binding. Journal of Biological Chemistry, 285(52), 40762-40770. https://doi.org/10.2210/pdb3o3u/pdb
Pinto, R. S., Minanni, C. A., de Araújo Lira, A. L., & Passarelli, M. (2022). Advanced glycation end products: A sweet flavor that embitters cardiovascular disease. International Journal of Molecular Sciences, 23(5), 2404. https://doi.org/10.3390/ijms23052404
Poznyak, A., Grechko, A. V., Poggio, P., Myasoedova, V. A., Alfieri, V., & Orekhov, A. N. (2020). The diabetes mellitus–atherosclerosis connection: The role of lipid and glucose metabolism and chronic inflammation. International Journal of Molecular Sciences, 21(5), 1835. https://doi.org/10.3390/ijms21051835
Pulido, R., Baker, S. J., Barata, J. T., Carracedo, A., Cid, V. J., Chin-Sang, I. D., ... & Leslie, N. R. (2014). A unified nomenclature and amino acid numbering for human PTEN. Science Signaling, 7(332), pe15. https://doi.org/10.1126/scisignal.2005560
Sala, L. L., Prattichizzo, F., & Ceriello, A. (2019). The link between diabetes and atherosclerosis. European Journal of Preventive Cardiology, 26(2_suppl), 15-24. https://doi.org/10.1177/2047487319878373
Setiani, L. A., Sari, B. L., & Muntaza, W. (2023). Prediction of Carcinogenic, Mutagenic, Hepatotoxic, and LD50 Toxicity of Herbs Euphorbia hirta and Camellia sinensis Leaf Compounds as In Silico Antihypertensive Agents. Jurnal Penelitian Pendidikan IPA, 9(SpecialIssue), 103-112. https://doi.org/10.29303/jppipa.v9iSpecialIssue.5900
Syahputra, G., Gustini, N., Bustanussalam, B., Hapsari, Y., Sari, M., Ardiansyah, A., ... & Putra, M. Y. (2021). Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia, 68, 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Vianello, E., Beltrami, A. P., Aleksova, A., Janjusevic, M., Fluca, A. L., Corsi Romanelli, M. M., ... & Dozio, E. (2025). The advanced glycation end-products (AGE)–receptor for AGE system (RAGE): An inflammatory pathway linking obesity and cardiovascular diseases. International Journal of Molecular Sciences, 26(8), 3707. https://doi.org/10.3390/ijms26083707
Wang, Y., Xing, J., Xu, Y., Zhou, N., Peng, J., Xiong, Z., ... & Jiang, H. (2015). In silico ADME/T modelling for rational drug design. Quarterly Reviews of Biophysics, 48(4), 488-515. https://doi.org/10.1017/S0033583515000190
Wu, Q., & Huang, S. Y. (2023). HCovDock: an efficient docking method for modeling covalent protein–ligand interactions. Briefings in Bioinformatics, 24(1), bbac559. https://doi.org/10.1093/bib/bbac559
Ye, J., Li, L., Wang, M., Ma, Q., Tian, Y., Zhang, Q., ... & Sun, G. (2022). Diabetes mellitus promotes the development of atherosclerosis: the role of NLRP3. Frontiers in Immunology, 13, 900254. https://doi.org/10.3389/fimmu.2022.900254
Aekthammarat, D., Pannangpetch, P., & Tangsucharit, P. (2019). Moringa oleifera leaf extract lowers high blood pressure by alleviating vascular dysfunction and decreasing oxidative stress in L-NAME hypertensive rats. Phytomedicine : International Journal of Phytotherapy and Phytopharmacology, 54, 9–16. https://doi.org/10.1016/j.phymed.2018.10.023
Al-Attas, O., Al-Daghri, N., Alokail, M., Abd-Alrahman, S., Vinodson, B., & Sabico, S. (2014). Metabolic benefits of six-month thiamine supplementation in patients with and without diabetes mellitus type 2. Clinical Medicine Insights: Endocrinology and Diabetes, 7, 1–6. https://doi.org/10.4137/CMED.S13573
Ameji, P. J., Uzairu, A., Shallangwa, G. A., & Uba, S. (2023). Molecular docking-based virtual screening, drug-likeness, and pharmacokinetic profiling of some anti-Salmonella typhimurium cephalosporin derivatives. Journal of Taibah University Medical Sciences, 18(6), 1417-1431. https://doi.org/10.1016/j.jtumed.2023.05.021
Auli, W. N., Husniati, H., Suprahman, N. Y., Fauziyya, R., Sarmoko, S., Ashari, A., ... & Fasya, G. A. (2024). Study of Gnetum gnemon metabolites as potential anti-breast and prostate cancer by metabolomic and molecular docking. Journal of Applied Pharmaceutical Science, 14(12), 120-130. https://dx.doi.org/10.7324/JAPS.2024.170723
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., ... & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235-242. https://doi.org/10.1093/nar/28.1.235
Brito, M. A. D. (2011). Pharmacokinetic study with computational tools in the medicinal chemistry course. Brazilian Journal of Pharmaceutical Sciences, 47, 797-805. https://doi.org/10.1590/S1984-82502011000400017
Bulusu, G., & Desiraju, G. R. (2020). Strong and weak hydrogen bonds in protein–ligand recognition. Journal of the Indian Institute of Science, 100(1), 31-41. https://doi.org/10.1007/s41745-019-00141-9
Ceriello, A., Gallo, M., Armentano, V., Perriello, G., Gentile, S., & De Micheli, on behalf of the Associazione Medici Diabetologi, A. (2012). Personalizing treatment in type 2 diabetes: A self-monitoring of blood glucose inclusive innovative approach. Diabetes Technology & Therapeutics, 14(4), 373-378. https://doi.org/10.1089/dia.2011.0233
Chavakis, T., Bierhaus, A., & Nawroth, P. P. (2004). RAGE (receptor for advanced glycation end products): A central player in the inflammatory response. Microbes and Infection, 6(13), 1219-1225. https://doi.org/10.1016/j.micinf.2004.08.004
Chumark, P., Khunawat, P., Sanvarinda, Y., Phornchirasilp, S., Morales, N. P., Phivthong-Ngam, L., ... & Pongrapeeporn, K. U. S. (2008). The in vitro and ex vivo antioxidant properties, hypolipidaemic and antiatherosclerotic activities of water extract of Moringa oleifera Lam. leaves. Journal of Ethnopharmacology, 116(3), 439-446. https://doi.org/10.1016/j.jep.2007.12.010
Ciftci, M. H., Turkoglu, V., Bas, Z., & Celikezen, F. C. (2024). In vitro inhibitor effect and molecular docking of thiamine (vitamin B1), riboflavin (vitamin B2), and reference inhibitor captopril on angiotensin-converting enzyme purified from sheep plasma. Archives of Physiology and Biochemistry, 130(6), 974-983. https://doi.org/10.1080/13813455.2024.2376814
Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
Dallakyan, S., & Olson, A. J. (2014). Small-molecule library screening by docking with PyRx. In Chemical biology: methods and protocols (pp. 243-250). New York, NY: Springer New York. https://doi.org/10.1007/978-1-4939-2269-7_19
De Freitas, R. F., & Schapira, M. (2017). A systematic analysis of atomic protein–ligand interactions in the PDB. Med. Chem. Commun., 8, 1970-1981. https://doi.org/10.1039/C7MD00381A
de Oliveira, T. A., Medaglia, L. R., Maia, E. H. B., Assis, L. C., de Carvalho, P. B., da Silva, A. M., & Taranto, A. G. (2022). Evaluation of docking machine learning and molecular dynamics methodologies for DNA-ligand systems. Pharmaceuticals, 15(2), 132. https://doi.org/10.3390/ph15020132
du Toit, E. S. (2019, November). Horticultural research review on Moringa oleifera trees growing in South Africa under sub-optimal conditions. In II International Symposium on Moringa 1306 (pp. 1-12). https://doi.org/10.17660/ActaHortic.2021.1306.1
Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules, 20(7), 13384-13421. https://doi.org/10.3390/molecules200713384
Gadaleta, D., Vuković, K., Toma, C., Lavado, G. J., Karmaus, A. L., Mansouri, K., ... & Roncaglioni, A. (2019). SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data. Journal of Cheminformatics, 11(1), 58. https://doi.org/10.1186/s13321-019-0383-2
Gu, Y., Zhang, X., Xu, A., Chen, W., Liu, K., Wu, L., ... & Luo, Q. (2023). Protein–ligand binding affinity prediction with edge awareness and supervised attention. Iscience, 26(1). https://doi.org/10.1016/j.isci.2022.105892
Guvatova, Z. G., Vakhrusheva, A., & Moskalev, A. (2025). A receptor for glycation end products (RAGE) is a key transmitter between garb-aging and inflammaging. Ageing Research Reviews, 113, 102919. https://doi.org/10.1016/j.arr.2025.102919
Indurthi, V. S., Jensen, J. L., Leclerc, E., Sinha, S., Colbert, C. L., & Vetter, S. W. (2020). The Trp triad within the V-domain of the receptor for advanced glycation end products modulates folding, stability and ligand binding. Bioscience Reports, 40(1), BSR20193360. https://doi.org/10.1042/BSR20193360
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2025). PubChem 2025 update. Nucleic Acids Research, 53(D1), D1516-D1525. https://doi.org/10.1093/nar/gkae1059
König, J., Müller, F., & Fromm, M. F. (2013). Transporters and drug-drug interactions: important determinants of drug disposition and effects. Pharmacological Reviews, 65(3), 944-966. https://doi.org/10.1124/pr.113.007518
Lang, S., Braz, N. F., Slater, M. J., & Kidley, N. J. (2025). In Silico Methods for Ranking Ligand–Protein Interactions and Predicting Binding Affinities: Which Method is Right for You? Journal of Medicinal Chemistry, 68(19), 19795-19799. https://doi.org/10.1021/acs.jmedchem.5c02582
Lin, H., Yang, Y., Wang, X., Chung, M., Zhang, L., Cai, S., ... & Pan, Y. (2025). Targeting the AGEs-RAGE axis: pathogenic mechanisms and therapeutic interventions in diabetic wound healing. Frontiers in Medicine, 12, 1667620. https://doi.org/10.3389/fmed.2025.1667620
Madushanka, A., Moura Jr, R. T., Verma, N., & Kraka, E. (2023). Quantum mechanical assessment of protein–ligand hydrogen bond strength patterns: insights from semiempirical tight-binding and local vibrational mode theory. International Journal of Molecular Sciences, 24(7), 6311. https://doi.org/10.3390/ijms24076311
Majewski, M., Ruiz-Carmona, S., & Barril, X. (2019). An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Communications Chemistry, 2(1), 110. https://doi.org/10.1038/s42004-019-0205-5
Nathan, D. M., Bayless, M., Cleary, P., Genuth, S., Gubitosi-Klug, R., Lachin, J. M., ... & DCCT/EDIC Research Group. (2013). Diabetes control and complications trial/epidemiology of diabetes interventions and complications study at 30 years: Advances and contributions. Diabetes, 62(12), 3976- 3986. https://doi.org/10.2337/db13-1093
Nivatya, H. K., Singh, A., Kumar, N., Sonam, Sharma, L., Singh, V., ... & Mishra, A. K. (2025). Assessing molecular docking tools: understanding drug discovery and design. Future Journal of Pharmaceutical Sciences, 11(1), 111. https://doi.org/10.1186/s43094-025-00862-y
Pantsar, T., & Poso, A. (2018). Binding affinity via docking: fact and fiction. Molecules, 23(8), 1899. https://doi.org/10.3390/molecules23081899
Park, H., & Boyington, J. C. (2010). The 1.5 Å crystal structure of human receptor for advanced glycation endproducts (RAGE) ectodomains reveals unique features determining ligand binding. Journal of Biological Chemistry, 285(52), 40762-40770. https://doi.org/10.2210/pdb3o3u/pdb
Pinto, R. S., Minanni, C. A., de Araújo Lira, A. L., & Passarelli, M. (2022). Advanced glycation end products: A sweet flavor that embitters cardiovascular disease. International Journal of Molecular Sciences, 23(5), 2404. https://doi.org/10.3390/ijms23052404
Poznyak, A., Grechko, A. V., Poggio, P., Myasoedova, V. A., Alfieri, V., & Orekhov, A. N. (2020). The diabetes mellitus–atherosclerosis connection: The role of lipid and glucose metabolism and chronic inflammation. International Journal of Molecular Sciences, 21(5), 1835. https://doi.org/10.3390/ijms21051835
Pulido, R., Baker, S. J., Barata, J. T., Carracedo, A., Cid, V. J., Chin-Sang, I. D., ... & Leslie, N. R. (2014). A unified nomenclature and amino acid numbering for human PTEN. Science Signaling, 7(332), pe15. https://doi.org/10.1126/scisignal.2005560
Sala, L. L., Prattichizzo, F., & Ceriello, A. (2019). The link between diabetes and atherosclerosis. European Journal of Preventive Cardiology, 26(2_suppl), 15-24. https://doi.org/10.1177/2047487319878373
Setiani, L. A., Sari, B. L., & Muntaza, W. (2023). Prediction of Carcinogenic, Mutagenic, Hepatotoxic, and LD50 Toxicity of Herbs Euphorbia hirta and Camellia sinensis Leaf Compounds as In Silico Antihypertensive Agents. Jurnal Penelitian Pendidikan IPA, 9(SpecialIssue), 103-112. https://doi.org/10.29303/jppipa.v9iSpecialIssue.5900
Syahputra, G., Gustini, N., Bustanussalam, B., Hapsari, Y., Sari, M., Ardiansyah, A., ... & Putra, M. Y. (2021). Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia, 68, 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Vianello, E., Beltrami, A. P., Aleksova, A., Janjusevic, M., Fluca, A. L., Corsi Romanelli, M. M., ... & Dozio, E. (2025). The advanced glycation end-products (AGE)–receptor for AGE system (RAGE): An inflammatory pathway linking obesity and cardiovascular diseases. International Journal of Molecular Sciences, 26(8), 3707. https://doi.org/10.3390/ijms26083707
Wang, Y., Xing, J., Xu, Y., Zhou, N., Peng, J., Xiong, Z., ... & Jiang, H. (2015). In silico ADME/T modelling for rational drug design. Quarterly Reviews of Biophysics, 48(4), 488-515. https://doi.org/10.1017/S0033583515000190
Wu, Q., & Huang, S. Y. (2023). HCovDock: an efficient docking method for modeling covalent protein–ligand interactions. Briefings in Bioinformatics, 24(1), bbac559. https://doi.org/10.1093/bib/bbac559
Ye, J., Li, L., Wang, M., Ma, Q., Tian, Y., Zhang, Q., ... & Sun, G. (2022). Diabetes mellitus promotes the development of atherosclerosis: the role of NLRP3. Frontiers in Immunology, 13, 900254. https://doi.org/10.3389/fimmu.2022.900254
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Thadeus, M., Ghanny, N., Citrawati, M., & Susantiningsih, T. (2026). Screening and Profiling of Bioactive Compounds from Moringa Oleifera Fruit Interaction with Advanced Glycation End Product Protein: A Molecular Docking Approach for Anti-Atherosclerosis Candidate Identification. International Journal of Advancement in Life Sciences Research, 9(1), 157-170. https://doi.org/https://doi.org/10.31632/ijalsr.2026.v09i01.012
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