Molecular Dynamics Simulation: Analysis of Mahogany Plant Compounds (Swietenia macrophylla King) against the ACE2 Enzyme of SARS-CoV-2

Lalu Sanik Wahyu Fadil Amrulloh; Ayudia Cipta  Khairani; Widayanti  Supraba; Siti Amalia Wahyu  Pratiwi; M. Ari  Wisnu

Authors

Lalu Sanik Wahyu Fadil Amrulloh Department of Pharmacy, Nahdlatul Ulama NTB University, Mataram, Indonesia
Ayudia Cipta Khairani Department of Pharmacy, Bumigora University, Mataram, Indonesia
Widayanti Supraba Department of Pharmacy, Nahdlatul Ulama NTB University, Mataram, Indonesia
Siti Amalia Wahyu Pratiwi Department of Pharmacy, Nahdlatul Ulama NTB University, Mataram, Indonesia
M. Ari Wisnu Department of Pharmacy, Nahdlatul Ulama NTB University, Mataram, Indonesia

Keywords:

ACE2, Molecular Dynamics Simulation, SARS-CoV-2, Swietenia macrophylla

Abstract

This study is a continuation of a previous study that analyzed the interaction of bioactive compounds from mahogany (Swietenia macrophylla King) with the SARS-CoV-2 Angiotensin-Converting Enzyme 2 (ACE2) using a molecular docking approach. This study aims to evaluate the dynamic stability of the ligand-protein complex through molecular dynamics simulation using YASARA Dynamics software with the AMBER14 force field for 100 ns. The parameters analyzed include Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). The results show that the ACE2-secomahoganin and ACE2-stigmasterol complexes experienced relatively high RMSD fluctuations, indicating global conformational changes in the protein structure during the simulation. Although RMSF analysis shows relatively low fluctuations in several active site residues such as His374, His378, Glu402, and Tyr515, the overall variability indicates that the system does not exhibit uniform stability. These findings provide preliminary computational insights into the dynamic interactions of mahogany compounds with ACE2, with stigmasterol showing relatively more consistent behavior than secomahoganin and may be potential candidates for further research against SARS-CoV-2, although further computational and experimental validation is required.

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