Docking studies for screening antibacterial compounds of Red Jeringau (Acorus calamus L.) using Shigella flexneri protein as a model system

Riyadh Aqilsya Amaryl Dyas; Bambang Wijianto; Hariyanto IH

doi:10.29303/aca.v6i2.161

Interaction of 50S Ribosomal Protein residues against ligand test (A) α-Asarone compound (B) β-Asarone

Studi docking untuk skrining senyawa antibakteri dari Jeringau Merah (Acorus calamus L.) menggunakan protein Shigella flexneri sebagai model sistem

Penulis

Riyadh Aqilsya Amaryl Dyas , Bambang Wijianto , Hariyanto IH

DOI:

10.29303/aca.v6i2.161

Diterbitkan:

2023-06-24

Terbitan:

Vol 6 No 2 (2023)

Kata Kunci:

Red Jeringau (Acorus calamus L.), α and β-Asarone, Antibacterial, Autodock VINA, ProTox-II5

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Dyas, R. A. A., Wijianto, B., & IH, H. (2023). Studi docking untuk skrining senyawa antibakteri dari Jeringau Merah (Acorus calamus L.) menggunakan protein Shigella flexneri sebagai model sistem. Acta Chimica Asiana, 6(2), 343–350. https://doi.org/10.29303/aca.v6i2.161

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Abstrak

Alfa dan Beta asarone diidentifikasi sebagai senyawa utama dari Jeringau merah (Acorus calamus L.) yang terkandung pada seluruh bagian tanaman dan diduga memiliki sifat antimikroba. Tujuan dari penelitian ini adalah untuk mengkaji mekanisme antibakteri kedua senyawa tersebut terhadap Shigella flexneri melalui studi penambatan molekul senyawa ligan alfa dan beta asarone terhadap protein PBP2 dan 50S Ribosomal Protein dengan AutoDock Vina. Protokol penambatan molekul menggunakan perangkat PyRx dilakukan dengan nilai Exhaustiveness = 106, grid x = 38.738375, y = 112.645792, z = 46.926417 untuk PBP2, dan grid x = 71.721251, y = 47.551601, z = 9.663173 terhadap 50S Ribosomal Protein. Hasil penambatan molekul pada senyawa alfa asarone diperoleh nilai afinitas sebesar -5,7 kcal/mol terhadap PBP2 dan nilai afinitas sebesar -5,6 kcal/mol terhadap 50S Ribosomal Protein, sedangkan beta asarone memiliki nilai afinitas sebesar -5,6 kcal/mol terhadap PBP2 dan nilai afinitas sebesar -5,7 kcal/mol pada 50S Ribosomal Protein. Dibandingkan dengan kontrol, afinitas alfa dan beta asarone bernilai lebih besar. Penambatan molekul senyawa alfa dan beta asarone menghasilkan ikatan ionik pada asam amino TYR529 dan ikatan polar pada asam amino ASN552 dari PBP2. Namun hanya beta asarone yang menghasilkan ikatan ionik pada asam amino ILE17 dan ikatan polar pada asam amino GLU13 dari 50S Ribosomal Protein. Berdasarkan penelitian ini, senyawa alfa dan beta asarone terbukti memiliki aktivitas antibakteri terhadap bakteri Shigella flexneri melalui gangguan permeabilitas dinding sel bakteri. Kedua senyawa juga diprediksi memiliki efek karsinogenik dan mutagenik.

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Studi docking untuk skrining senyawa antibakteri dari Jeringau Merah (Acorus calamus L.) menggunakan protein Shigella flexneri sebagai model sistem

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