Profiling Bioactive Compounds and Antimicrobial Potential of Clove (Syzygium aromaticum L.) Varieties of Sikotok, Siputih, and Zanzibar Extracts Using Gas Chromatography-Mass Spectrometry and Molecular Docking Analysis

Kiramang, Khaerani; Alam, Gemini; Natsir, Asmuddin; Purwanti, Sri; Mujnisa, A.

doi:10.21608/ejchem.2025.327043.10604

Profiling Bioactive Compounds and Antimicrobial Potential of Clove (Syzygium aromaticum L.) Varieties of Sikotok, Siputih, and Zanzibar Extracts Using Gas Chromatography-Mass Spectrometry and Molecular Docking Analysis

Document Type : Original Article

Authors

¹ Faculty of Science and Technology, Islamic State of Alauddin University, Makassar, 92118, Indonesia

² Department of Pharmacognosy-Phytochemistry, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia

³ Faculty of Animal Science, Hasanuddin University, Makassar, 90245, Indonesia

10.21608/ejchem.2025.327043.10604

Abstract

Clove (Syzygium aromaticum L.) is widely recognized for its rich phytochemical profile and traditional use as a natural remedy with antimicrobial properties. This study aimed to investigate the phytochemical composition of 3 clove varieties, namely Sikotok, Siputih, and Zanzibar using gas chromatography-mass spectrometry (GC-MS). The potential antimicrobial compounds were evaluated through in molecular docking studies against Staphylococcus aureus (3U2D) and Escherichia coli (6NTZ) proteins. Clove extracts from young, mature, and fallen leaves were subjected to GC-MS analysis to identify bioactive compounds, focusing on those with a relative abundance greater than 1%. A total of 12 compounds were identified, with significant variations in relative abundances and retention times. The major compounds detected across all varieties were m-eugenol (25.65-58.49%), caryophyllene (7.63-14.39%), and hexatriacontane (0.59-43.184%). Other compounds, such as eugenol, humulene, α-farnesene, eugenol acetate, caryophyllene oxide, sandaracopimaradiene, lupeol, squalene, and nonacosane, were detected in selected samples. The result of molecular docking showed that α-farnesene (-7.2 kcal/mol and -7.4 kcal/mol), sandaracopimaradiene (-6.8 kcal/mol and -6.3 kcal/mol), and eugenol acetate (-6.2 kcal/mol) had significant binding affinities to target proteins 3U2D and 6NTZ, with other major compounds showing binding energies ranging from 5.5 to 5.8 kcal/mol. In conclusion, this study showed the importance of the clove variety in enhancing the antimicrobial potential of extracts, particularly with the Sikotok and Zanzibar varieties, which had higher concentrations of phenolic compounds and terpenoids in young leaves. These results provided valuable insights into the future applications of natural antimicrobial agents.

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