Molecular Dynamics Simulation of Ecdysone from Sida rhombifolia Against PBP2a Protein of MRSA as a Potential New Antibacterial Candidate

Mohammad Firdaus Alshol; Rina Herowati; Ismi Rahmawati

doi:10.55927/fjmr.v4i10.555

Authors

Mohammad Firdaus Alshol Setia Budi University
Rina Herowati Setia Budi University
Ismi Rahmawati Setia Budi University

DOI:

https://doi.org/10.55927/fjmr.v4i10.555

Keywords:

Molecular Dynamics, Ecdysone, Sida Rhombifolia

Abstract

This study aims to evaluate the predicted binding stability of the compound ecdysone in comparison with the native ligand, in order to determine its potential as an effective and stable antibacterial agent through molecular docking and molecular dynamics (MD) simulations. An exploratory computational approach was employed to assess the antibacterial activity, interaction patterns, and stability of compounds derived from Sida rhombifolia. A total of 15 bioactive compounds were docked against the molecular target PBP2a (PDB ID: 4JCN) using AutoDockTools and PyMol, followed by an analysis of amino acid residue similarity between each test ligand and the native ligand. The compound exhibiting the best interaction profile was further analyzed using MD simulation to evaluate its binding stability and pharmacokinetic properties. Validation parameters, including Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF), were calculated based on in silico predictions. MD simulations were conducted using YASARA Dynamics. The molecular docking results indicated that ecdysone demonstrated the highest binding affinity and interaction pattern comparable to that of the native ligand. The MD simulation further confirmed that ecdysone maintained stable binding throughout the simulation period, as reflected by RMSD and RMSF profiles of the MRSA target complex.

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