The target of SARS-CoV-2: Analysis of N3 ligand binding energy vs. natural compounds (curcumin) using molecular dynamics of force fields CHARMM

Abstract

SARS-CoV-2 has been an endemic disease until now, but scientists are still trying to find an effective drug. Research has been carried out to find drugs that are effective against SARS-CoV-2. Mpro is used as the main target to be attacked. A natural compound test ligand (curcumin) was used anda compared with the N3 ligand. This research used molecular dynamics methods to identify and study inhibitor binding interactions. Molecular dynamics simulation using software Gromacs with CHARMM force field at 1000 kJ/mol and 300 K/1 bar conditions. This research will analyze the trajectory of the simulation results for the value of RMSD, RMSF, and Rg, which emphasizes the conditions of balance and compactness. The drug-binding affinity of the main protease SARS-CoV-2 was analyzed using the MM/PBSA method. An enormous free energy value will indicated the strength of the interaction between SARS-CoV-2 and the N3/curcumin ligand. From the results, it can be seen that the total interaction energy of the N3-protein ligand is -333.717 kJ/mol, and that of the curcumin-protein ligand is -0.023 kJ/mol. Meanwhile, based on the value of free energy on N3-protein is -28.566 kJ/mol and curucumin-protein 9.477 kJ/mol. Thus, this study showed that the N3 ligand was more effective than the curcumin ligand in binding to the main protease of SARS-CoV-2. © 2022 Author(s).