MOLECULAR DOCKING AND THEORETICAL TOXICITY ASSESSMENT OF BIOACTIVE CONSTITUENTS OF LEAF AND ROOT BARK ESSENTIAL OILS FROM Spondia dulcis
DOI:
https://doi.org/10.33003/fjs-2026-1003-4601Keywords:
Antioxidant, Essential oil, Molecular docking, Spondia dulcis, ToxicityAbstract
Spondias dulcis (S. dulcis) belongs to the Anacardiaceae family that is also called Ambarella or golden apple. The medicinal uses of the plant have been reported. This study was conducted to investigate the phytochemical profile, antioxidant activity and the in silico drug discovery capability of the essential oil of the leaf and root bark of Spondia dulcis. Essential oils were obtained by hydro-distillation, and their compositions were determined using gas chromatography-mass spectrometry (GC-MS). The essential oil of the leaf (SDLEO) was found to be comprised of 30 compounds, with linalool and trans-β-ionone as major constituents, with concentrations of 35.06 and 11.48% respectively. In contrast, the SDREO contained 19 compounds, comprising p-cymene (44.03%) and o-acetyl-p-cresol (14.36%) as major compounds. Theoretical toxicity prediction on the pkCSM platform showed that several compounds were non-hepatotoxic and non-carcinogenic. Molecular docking of the antioxidant protein xanthine oxidase (PDB ID: 3NRZ) demonstrated good binding affinities, in which neophytadiene -5.6 kcal/mol) and farnesol -5.4 kcal/mol) had good binding affinities as compared to ascorbic acid -5.8 kcal/mol). These results indicate that S. dulcis essential oils displayed high antioxidant activity, and they contain bioactive non-toxic constituents for future pharmacological development.
References
Abdulrahman, M. D., Hamad S.W., Usman M., Tahir, S.M., Sunusi, N., & Yunusa, A., (2021). Therapeutic plants used for Typhoid Fever treatment in Kaduna State Nigeria. Al-Qadisiyah Journal of Pure Science (QJPS), 26(3), 9-21.
Adwas, A. A., Elsayed, A., Azab, A. E., & Quwaydir, F. A. (2019). Oxidative stress and antioxidant mechanisms in human body. J. Appl. Biotechnol. Bioeng, 6(1), 43-47.
Agu, P. C., Nduneseokwu, N. C., Nwiziogo, F. C., Okafor, M. U., Alum, E. U., Egwu, C. O., Anidu, I.C., Ezinwa, C.A,, Ibiam A.U., & Aja, P. M. (2025). Historical and ethnopharmacological perspectives on African medicinal plants: From traditional remedies to computational drug discovery. Scientific African, 30, e02941.
Ahmed, M. H., Singh, G., Castrosanto, M., Hossain, A., Rifat, M. M. I., Rima, S. H., Gupta, V, Kesharwani, R. K, Jaremko, M, Emwas, A. H, Alam, P. A., & Azam, F. (2024). A structure-based drug design approach for the identification of antiviral compounds targeting the chikungunya virus RdRp protein. Chemical Physics Impact, 8, 100450.
Al-Kufaishi, A. M., & Al-Musawi, N. J. (2025). Oxidative stress and related diseases: a comprehensive review. Journal of Preventive, Diagnostic and Treatment Strategies in Medicine, 4(2), 65-70.
Aloke, C., Egwu, C. O., Adelusi, O. A., Chinaka, N., Kanu, C., Ogbodo, P. N., Akumadu B.O., & Achilonu, I. (2023). Medicinal plants: A promising source of anti-diabetic agents in sub-Sahara Africa. Current Issues in Pharmacy and Medical Sciences, 36(2), 65-76.
Ansari, R. M., Mundke, R. N., Agrawal, Y. O., et al. (2025). Recent advances in molecular docking techniques: Transforming perspectives in distinct drug targeting and drug discovery approaches. Medicinal Chemistry (Shariqah, United Arab Emirates). Advance online publication. https://doi.org/10.2174/0115734064384472250716144736
Ardjani, A. T. E., & Mekelleche, S. M. (2017). Theoretical investigation and molecular docking approach on the antioxidant activity of Schiff bases and their tautomers. Journal of Theoretical and Computational Chemistry, 16(01), 1750001.
Ayodele, P. F., Bamigbade, A., Bamigbade, O. O., Adeniyi, I. A., Tachin, E. S., Seweje, A. J., & Farohunbi, S. T. (2023). Illustrated procedure to perform molecular docking using PyRx and Biovia discovery studio visualizer: a case study of 10kt with atropine. Progress in Drug Discovery & Biomedical Science, 6(1).
Bhat, A. S., Ahmed, M., Abbas, K., Mustafa, M., Alam, M., Salem, M. A., Islam, S., Tantry, I. Q., Singh, Y., & Fatima, M. (2024). Cancer initiation and progression: a comprehensive review of carcinogenic substances, anti-cancer therapies, and regulatory frameworks. Asian J Res Biochem, 14(4), 111-25.
Chikhale, R. V., Pawar, S. P., Kolpe, M. S., Shinde, O. D., Dahlous, K. A., Mohammad, S., Patil, P.C. & Bhowmick, S. (2024). Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies. Molecular Diversity, 28(4), 1947-1964.
Cruz, B. G., de Freitas, T. S., Costa, M. D. S., da Silva, A. R. P., Coutinho, H. D. M., de Morais, S. M., Marinho, E. S, Teixeira, A. M, & Silva dos Santos, H. (2023). Chemical Composition, Antibacterial and Inhibitory Activity of the Efflux Pump of Essential Oils from Croton piauhiensis Müll. Nutraceuticals, 3(4), 591-604.
Cunha, C., Ribeiro, H. M., Rodrigues, M., & Araujo, A. R. (2022). Essential oils used in dermocosmetics: Review about its biological activities. Journal of Cosmetic Dermatology, 21(2), 513-529.
Dev, A. A., & Mol, J. S. (2024). Volatile chemical profiling and distinction of Citrus essential oils by GC analyses with correlation matrix; evaluation of its in vitro radical scavenging and microbicidal efficacy. Results in Chemistry, 7, 101460.
Dodoš, T., Novaković, J., Vujisić, L., Marin, P. D., & Rajčević, N. (2024). Geographic variability of winter savory essential oil. Industrial Crops and Products, 210, 118167.
Ekoro, I. A., Odeja, O. O., Osharode, M. E., Tade, O. O., Omadoko, O., Caesar, A. T., & Ehigiator, S. (2025). Molecular Docking, Normal Mode Analysis and Quantum Chemical Investigations of selected Isoxazole-diphenylamine Hybrids as Potential Antioxidants. In Silico Research in Biomedicine, 100107.
Fernandes, F. H. A., Soares, S. D. S., Bekbolatova, E., Boylan, F., & Salgado, H. R. N. (2024). Pharmacological, toxicological and phytochemical analysis of Spondias dulcis parkinson. Natural Product Research, 38(6), 1049-1053.
Fillipova, A. A., Szhenova, T. M., Bokov, D. O., Golovina, N. V., Garnova, N. Y., & Dobrokhotov, D. A. (2021). Gas Chromatography Quantification of Geraniol in a Dental Hydrogel Containing the Essential Oil of Pelargonium graveolens. Moscow University Chemistry Bulletin, 76(2), 137-146.
Gentile, D., Floresta, G., Patamia, V., Chiaramonte, R., Mauro, G. L., Rescifina, A., & Vecchio, M. (2020). An integrated pharmacophore/docking/3D-QSAR approach to screening a large library of products in search of future botulinum neurotoxin A inhibitors. International journal of molecular sciences, 21(24), 9470.
Gomasta, J., Sarker, B. C., Alam, A., Kayesh, E., Islam, M., Khan, H. I., & Rahman, M. M. (2025). Floral biology and reproductive phenology of golden apple (Spondias dulcis Frost.) in subtropical terrace soil condition. Discover Plants, 2(1), 67.
Gu, Y., Yu, Z., Wang, Y., Chen, L., Lou, C., Yang, C., Li W, Liu G., & Tang, Y. (2024). admetSAR3. 0: a comprehensive platform for exploration, prediction and optimization of chemical ADMET properties. Nucleic acids research, 52(W1), W432-W438.
Günther, A., & Bednarczyk-Cwynar, B. (2025). Oleanolic Acid: A promising antioxidant—sources, mechanisms of action, therapeutic potential, and enhancement of bioactivity. Antioxidants, 14(5), 598.
Hariyono, P., Dwiastuti, R., Yusuf, M., Salin, N. H., & Hariono, M. (2022). 2-Phenoxyacetamide derivatives as SARS-CoV-2 main protease inhibitor: In silico studies. Results in Chemistry, 4, 100263.
Ibok, M. G., Odeja, O. O., Okpala, E. O., Eghwubare, J. E., & Anifalaje, E. O. (2023). E remomastax speciosa (Hochst.): GC/MS profiling, antioxidant and antimicrobial activities of stem essential oil. Future Journal of Pharmaceutical Sciences, 9(1), 51.
Islam, A., Jena, D., Mondal, N. S., Teli, A., Mondal, S., & Gautam, M. K. (2025). In-silico approaches for drug designing technology: Bridging discovery and development. Current Drug Discovery Technologies, 22(5), E15701638326869.
Jiang, H., Li, J., Wang, L., Wang, S., Nie, X., Chen, Y., Fu, Q., Jiang, M, Fu, C ... & He, Y. (2020). Total glucosides of paeony: a review of its phytochemistry, role in autoimmune diseases, and mechanisms of action. Journal of Ethnopharmacology, 258, 112913.
Joujeh, R., & Joujeh, D. (2024). Chemical Composition, Antibacterial and Antioxidant Activities of Some Lamiaceae Essential Oils. Journal of King Abdulaziz University: Science, 34(1).
Kıran, T. R., Otlu, O., & Karabulut, A. B. (2023). Oxidative stress and antioxidants in health and disease. Journal of Laboratory Medicine, 47(1), 1-11.
Kumar, P., Alpana, A., Dinesh, C., & Abhinav, B. (2020). In silico screening and molecular docking of bioactive agents towards human coronavirus receptor. GSC Biol Pharm Sci, 11, 132-40.
Lawal, I. O., Rafiu, B. O., Ale, J. E., Majebi, O. E., & Aremu, A. O. (2022). Ethnobotanical survey of local flora used for medicinal purposes among indigenous people in five areas in Lagos State, Nigeria. Plants, 11(5), 633.
Makangara, J. J., Mshandete, A. M., Mbega, E. R., Nyika, J. R., Mbago, F., Ndilanha, E. G., Nyika R. J., & Nyika, J. J. (2024). Review on the secondary metabolites, biological properties, and ethnomedicinal uses of the component species of the buheri wa afya formula used to treat COVID-19 in Tanzania. Phytomedicine Plus, 4(1), 100508.
Mansour, M. A., AboulMagd, A. M., & Abdel-Rahman, H. M. (2020). Quinazoline-Schiff base conjugates: in silico study and ADMET predictions as multi-target inhibitors of coronavirus (SARS-CoV-2) proteins. RSC advances, 10(56), 34033-34045.
Mehdizadeh, L., & Moghaddam, M. (2018). Essential oils: Biological activity and therapeutic potential. In Therapeutic, probiotic, and unconventional foods (pp. 167-179). Academic Press.
Mohammed, M., Bridgemohan, P., Mohamed, M. S., Bridgemohan, R. S. H., & Mohammed, Z. (2017). Postharvest physiology and storage of golden apple (Spondias cythera sonnerat or Spondias dulcis forst): a review. J Food Process Technol, 8(707), 2.
Monib, P. N. A. W., & Monib, A. W. (2024). The role of plants in traditional and modern medicine. Journal of Pharmacognosy and Phytochemistry, 13(2), 643-647.
Noshirvani, N. (2024). Essential oils as natural food preservatives: special emphasis on antimicrobial and antioxidant activities. Journal of food Quality, 2024(1), 5807281.
Okpala, E. O., Anthony, W. O., Eneogwe, G. O., Odeja, O. O., Ibok, M. G., Onoja, J. O., Odewo, S. A., Ike, S. N., Onanuga, O. A, & Semire, B. (2024). In vitro and in silico evaluation of the antimicrobial potential of Celtis zenkeri roots volatile metabolites. Eclética Química, 49.
Oyeyemi, A. W., Owonikoko, W. M., Okoro, T. D., Adagbonyi, O., & Ajeigbe, K. O. (2024). Water contamination: A culprit of serum heavy metals concentration, oxidative stress and health risk among residents of a Nigerian crude oil-producing community. Toxicology Reports, 12, 375-388.
Paul, S., El Bethel Lalthavel Hmar, J. H., & Zothantluanga, H. K. S. (2020). Essential oils: A review on their salient biological activities and major delivery strategies. Microcirculation, 5(9).
Petretto, G. L., Vacca, G., Addis, R., Pintore, G., Nieddu, M., Piras, F., Sogos V, Fancello F, Zara S., & Rosa, A. (2023). Waste Citrus limon leaves as source of essential oil rich in limonene and citral: Chemical characterization, antimicrobial and antioxidant properties, and effects on cancer cell viability. Antioxidants, 12(6), 1238.
Pino, S., Espinoza, L., Jara-Gutiérrez, C., Villena, J., Olea, A. F., & Díaz, K. (2023). Study of cannabis oils obtained from three varieties of C. sativa and by two different extraction methods: Phytochemical characterization and biological activities. Plants, 12(9), 1772.
Pradhan, D., Biswasroy, P., Haldar, J., Cheruvanachari, P., Dubey, D., Rai, V. K., Kar B, Kar, D. M, Rath, G., & Ghosh, G. (2022). A comprehensive review on phytochemistry, molecular pharmacology, clinical and translational outfit of Ocimum sanctum L. South African Journal of Botany, 150, 342-360.
Pyka, P., Garbo S, Murzyn, A., Satała, G., Janusz, A., Górka, M., Pietruś, W., Mituła, F., Popiel, D., Wieczorek, M., Palmisano, B., Raucci, A., Bojarski, A.J., Zwergei, C., Szymanska, E., Kucwaj-Brysz, K., Battistelli, C., Handzlik, J., & Podlewska, S. (2024). Unlockin,g the potential of higher-molecular-weight 5-HT7R ligands: Synthesis, affinity, and ADMET examination. Bioorganic Chemistry, 151, 107668.
Rajeshkumar, R. R., Kumar, B. K., Parasuraman, P., Panneerselvam, T., Sundar, K., Ammunje, D. N., Pandian, S.R.K., Murugesan, S., Kabilan, S.J.K., & Kunjiappan, S. (2022). Graph theoretical network analysis, in silico exploration, and validation of bioactive compounds from Cynodon dactylon as potential neuroprotective agents against α-synuclein. BioImpacts: BI, 12(6), 487.
Shaji, D., Das, A., Suzuki, R., Nagura, Y., Sabishiro, H., & Kurita, N. (2023). Proposal of novel ApoE4 inhibitors from the natural spice Cinnamon for the treatment of Alzheimer's disease: Ab initio molecular simulations. Biophysical Chemistry, 296, 106990.
Shao, C. Y., Zhang, Y., Lv, H. P., Zhang, Z. F., Zeng, J. M., Peng, Q. H., Zhu Y., & Lin, Z. (2022). Aromatic profiles and enantiomeric distributions of chiral odorants in baked green teas with different picking tenderness. Food Chemistry, 388, 132969.
Sheng, M. Y, Peng, D. W., Peng, H. M., Zhang, Y. L., Xiao, L., Zhang, M. R., Wang, S. Y, Zhao, C. P., Zhu, S. Y., Lu, J. K, Lin, L. Huang, R., Nie, J., & Fang, J. B. (2024). Effective substances and molecular mechanisms guided by network pharmacology: An example study of Scrophulariae Radix treatment of hyperthyroidism and thyroid hormone-induced liver and kidney injuries. Journal of Ethnopharmacology, 326, 117965.
Sinan, K. I., Zengin, G., Zheleva-Dimitrova, D., Gevrenova, R., Picot-Allain, M. C. N., Dall’Acqua, S., Behl, T, Goh, B. H, Ying, P. T., & Mahomoodally, M. F. (2021). Exploring the chemical profiles and biological values of two Spondias species (S. dulcis and S. mombin): Valuable Sources of Bioactive Natural Products. Antioxidants, 10(11), 1771.
Singh, S., Chaurasia, P. K., Bharati, S. L., & Golla, U. (2022). A mini-review on the safety profile of essential oils. MOJ Biol. Med, 7, 33-36.
Sutomo, S., & Pratama, M. R. F. (2020). Measuring the potential antioxidant activity of methyl gallate: Molecular docking study. Thai Journal of Pharmaceutical Sciences (TJPS), 44(1).
Tejada-Muñoz, S., Cortez, D., Rascón, J., Chavez, S. G., Caetano, A. C., Díaz-Manchay, R. J., Sandoval-Bances J, Huyhua-Gutierrez S, Gonzales L, Chenet SM., & Tapia-Limonchi, R. (2024). Antimicrobial activity of Origanum vulgare essential oil against Staphylococcus aureus and Escherichia coli. Pharmaceuticals, 17(11), 1430.
Tian, H., Ketkar, R., & Tao, P. (2022). Accurate admet prediction with xgboost. arXiv preprint arXiv:2204.07532.
Valdés, A., Sánchez-Martínez, J. D., Gallego, R., Ibáñez, E., Herrero, M., & Cifuentes, A. (2024). In vivo neuroprotective capacity of a Dunaliella salina extract-comprehensive transcriptomics and metabolomics study. npj Science of Food, 8(1), 4.
Zongo, A. W. S., Jin, C., Hao, G., Yu, N., Zogona, D., Nie, X., Lu, Y., Ye, Q., & Meng, X. (2024). Functional compounds of Torreya grandis nuts and their processing byproducts: Extraction process, health benefits, and food applications–A comprehensive review. Food Research International, 197, 115232.
Downloads
Published
Issue
Section
Categories
License
Copyright (c) 2026 Israel Azogor Ekoro, Oluwakayode Olubunmi Odeja

This work is licensed under a Creative Commons Attribution 4.0 International License.