Pengaruh Minimisasi Energi MMFF94 dengan MarvinSketch dan Open Babel PyRx pada Penambatan Molekular Turunan Oksindola Tersubstitusi

Atika Umi Hanif, Prima Agusti Lukis, Arif Fadlan

Abstract


 

In silico technique is widely used for drug discovery because it can predict the conformation of ligands in protein macromolecules and it can calculate the binding affinity. The energy minimization is carried out to make the ligand more stable near the initial state during molecular docking process. The Merck Molecular Force Field (MMFF94) is one type of energy minimization process often used in organic compounds. The molecular docking of substituted oxindole derivatives on indoleamine macromolecules 2,3-dioxygenase (IDO-1, PDB: 2D0T) by MMFF94 minimization operated by MarvinSketch and Open Babel in PyRx showed different results. The binding affinity energy obtained was also quite different, but the ligands have the same conformation and bind the same residue with slightly different bond distances.

 

Keywords: Molecular docking, energy minimization, substituted oxindole, Merck Molecular Force Field 94

 

 

Teknik in silico banyak digunakan untuk penemuan senyawa obat karena dapat memprediksi konformasi suatu ligan dalam makromolekul protein dan mampu menghitung nilai afinitas ikatan. Proses minimisasi energi dilakukan untuk menjadikan ligan lebih stabil mendekati keadaan awal selama penambatan molekular berlangsung. Merck Molecular Force Field (MMFF94) adalah salah satu jenis persamaan minimisasi energi yang sering digunakan pada senyawa organik. Hasil pengujian pengaruh minimisasi energi dengan MMFF94 menggunakan program MarvinSketch dan Open Babel dalam PyRx pada turunan oksindola tersubstitusi alkil terhadap makromolekul 2,3-dioxygenase indoleamine (IDO-1, PDB: 2D0T) menunjukkan hasil dengan nilai yang berbeda. Energi afinitas ikatan yang didapatkan juga cukup berbeda, namun ligan memiliki konformasi yang sama dan mengikat residu yang sama dengan jarak ikatan yang sedikit berbeda.

 

Kata kunci: Penambatan molekular, minimisasi energi, oksindola tersubstitusi, Merck Molecular Force Field 94

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DOI: https://doi.org/10.18860/al.v8i2.10481

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