POTENSI TAMANU (Calophyllum inophyllum) SEBAGAI INHIBITOR SARS-CoV-2 MENGGUNAKAN MOLECULAR DOCKING DAN SIMULASI MOLECULAR DYNAMIC

Rena, Suci Ramda (2025) POTENSI TAMANU (Calophyllum inophyllum) SEBAGAI INHIBITOR SARS-CoV-2 MENGGUNAKAN MOLECULAR DOCKING DAN SIMULASI MOLECULAR DYNAMIC. S2 thesis, University of Andalas.

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Abstract

Covid-19, caused by the SARS-CoV-2 virus, has been a global threat since the end of 2019. One of the main targets in drug design for developing antivirals against SARS-CoV-2 is the main protease (Mpro), a protein that plays a crucial role in the virus replication process. This research aims to identify the potential of triterpenoid compounds from tamanu (Canophyllum inophyllum) as SARS-CoV-2 inhibitors using an in-silico approach, employing molecular docking and molecular dynamics simulation methods. A total of ten triterpenoid compounds were selected and docked against the SARS-CoV-2 Mpro with the PDB ID code: 6W63 using Autodock-GPU on Google Colab. The results of the molecular docking indicated that oleanolic acid yielded the lowest binding affinity value of -8,2 kcal/mol, which suggests a strong binding affinity with the active site of the target protein. Furthermore, the oleanolic acid-6W63 complex was further analyzed using the molecular dynamics simulation method for 10 ns using OpenMM on Google Colab. The simulation results showed that the complex had good structural stability, as indicated by the relatively stable Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and radius of gyration (Rg) values throughout the simulation. These findings indicate that oleanolic acid has the potential as a promising anti-SARS-CoV-2 candidate. This study provides an initial contribution to the further development of Covid-19 therapy using natural materials through a computational approach.

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