Penambatan Molekul dan Simulasi Dinamika Molekular Kandungan Minyak Kayu Manis dan Minyak Serai Dapur Sebagai Antibakteri Methicillin Resistant Staphylococcus aureus

Caesart Leonardo Kaharudin, Afif Akmal Afkauni, Aditya Yuan Pramudyansyah, Niko Prasetyo

Abstract

Meluasnya penyebaran Methicillin Resistant Staphylococcus aureus (MRSA) yang kebal terhadap antibiotik β-laktam membuat penelitian untuk menemukan senyawa aktif yang memiliki potensi sebagai antibakteri MRSA menjadi penting. Salah satu penelitian yang dapat dilakukan adalah studi penambatan molekul. Studi penambatan molekul telah dilakukan menggunakan senyawa bahan alam dari minyak kayu manis dan minyak serai dapur dengan reseptor enzim Penicillin Binding Protein 2a (PBP2a). Studi ini memiliki tujuan untuk memprediksi kemampuan senyawa bahan alam dari kedua minyak atsiri tersebut sebagai antibakteri MRSA. Penambatan molekul dilakukan menggunakan perangkat lunak (software) AutoDock 4.2. Hasil penelitian menunjukkan bahwa senyawa dengan potensi sebagai antibakteri paling besar adalah trans-β-kariofilen dan geranil asetat dengan energi ikat sebesar -6,12 dan -5,11 kkal/mol dan konstanta inhibisi sebesar 32,69 dan 180,41 µM. Hasil penambatan molekul kemudian dilanjutkan dengan simulasi dinamika molekular. Hasil simulasi dinamika molekular menunjukkan bahwa kedua senyawa memiliki nilai Root Mean Square Deviation (RMSD) yang tinggi.

Molecular Docking and Molecular Dynamics Simulation of Cinnamon Oil and Kitchen Lemongrass Oil as Antibacterial Agent Against Methicillin-Resistant Staphylococcus aureus. The spread of Methicillin-Resistant Staphylococcus aureus (MRSA) caused the research for its antibiotic to become more pressing than ever. One of the research that can be conducted is a molecular docking study. A molecular docking study of natural products from cinnamon and lemongrass oil with Penicillin Binding Protein 2a (PBP2a) enzyme was conducted. This study aims to predict the ability of each natural product to become an MRSA antibiotic. The molecular docking was conducted with AutoDock 4.2 software. The result shows that β-caryophyllene and geranyl acetate have the most potential to become MRSA antibiotics with binding energies of -6.12 kcal/mol and -5.11 kcal/mol and inhibition constants of 32.69 μM and 180.41 µM, respectively. The results of molecular docking were validated using molecular dynamic simulation. Molecular dynamic simulation shows that both complexes have a high root mean square deviation (RMSD) value.

Keywords

antibiotic; natural product; MRSA; molecular docking.

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References

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DOI: https://doi.org/10.20961/alchemy.18.2.54997.140-147

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