Judul: In-silico Antibacterial Activity Analysis of Trigona Honey Secondary Metabolite Compounds Against Escherichia coli
Abstrak: Kasus keracunan pangan dapat disebabkan oleh cemaran mikrobiologis. Salah satu cara penanganan keracunan pangan karena cemaran mikrobiologis adalah dengan mengonsumsi madu. Madu memiliki aktivitas antibakteri yang dipengaruhi oleh beberapa faktor, salah satunya keberadaan metabolit sekunder. Jenis madu lebah tanpa sengat (Trigona) memiliki kandungan senyawa yang lengkap dan kompleks. Penelitian ini bertujuan menganalisis aktivitas antibakteri senyawa metabolit sekunder madu Trigona secara in-silico dan mengidentifikasi senyawa dengan aktivitas antibakteri terbaik terhadap E. coli. Metode penelitian mencakup pencarian senyawa, preparasi protein, validasi reseptor, preparasi senyawa uji, dan molecular docking. Hasil penelitian menunjukkan bahwa nilai ΔG native ligand sebesar -11,6 kkal/mol serta senyawa pembanding azithromycin -5,4 kkal/mol dan fluoroquinolone -7,4 kkal/mol. Lima senyawa uji dengan nilai ΔG terbaik, yaitu myricitrin (-10,7 kkal/mol); quercetrin (-10,3 kkal/mol); chlorogenic acid (-9,9 kkal/mol); rutin (-9,2 kkal); dan catechin (-9,0 kkal/mol) memiliki nilai yang lebih besar dibandingkan dengan native ligand, tetapi lebih kecil dibandingkan dengan senyawa pembanding. Semakin negatif nilai ΔG suatu senyawa, maka semakin kuat interaksi ikatan dengan reseptor dan semakin besar juga potensi aktivitas antibakterinya. Senyawa dengan kemiripan residu asam amino paling banyak dengan native ligand adalah 2-hydroxycinnamic acid (78,95%); ellagic acid, quercetrin, dan rutin (47,37%); serta 2,4-dihydroxybenzoic acid, myricitrin, salicylic acid, dan sinapic acid (42,11%). Semakin banyak residu asam amino yang sama dengan native ligand maka semakin baik aktivitas antibakteri senyawa tersebut. Senyawa dengan aktivitas antibakteri terbaik adalah myricitrin., Food poisoning cases can be caused by microbiological contamination. One way to handle food poisoning due to microbiological contamination is by consuming honey. Honey possesses antibacterial activity influenced by various factors, one of which is the presence of secondary metabolites. Stingless bee honey (Trigona) contains a comprehensive and complex range of compounds. This research aimed to analyze the in-silico antibacterial activity of secondary metabolite compounds in Trigona honey and identified the compounds with the best antibacterial activity. The research method included compound search, protein preparation, receptor validation, test compound preparation, and molecular docking. The research results showed that the ΔG value of the native ligand was -11.6 kcal/mol, while the reference compounds azithromycin and fluoroquinolone had ΔG values of -5.4 kcal/mol and -7.4 kcal/mol, respectively. The top five test compounds with the best ΔG values were myricitrin (-10.7 kcal/mol), quercetrin (-10.3 kcal/mol), chlorogenic acid (-9.9 kcal/mol), rutin (-9.2 kcal/mol), and catechin (-9.0 kcal/mol). These values were higher than the native ligand but lower than the reference compounds. The more negative the ΔG value of a compound, the stronger the binding interaction with the receptor and the greater the potential antibacterial activity. Compounds with the highest similarity in amino acid residues to the native ligand included 2-hydroxycinnamic acid (78.95%); ellagic acid, quercetrin, and rutin (47.37%); as well as 2,4-dihydroxybenzoic acid, myricitrin, salicylic acid, and sinapic acid (42.11%). The more amino acid residues were similar to the native ligand, the better the antibacterial activity of the compound. The compound with the best antibacterial activity was myricitrin.
Keyword: antibacterial, in-silico, molecular docking, secondary metabolite, stingless bee honey