The Molecular Docking and Molecular Dynamics Simulation of Some HIV-1 protease Inhibitors For the treatment of Coronavirus Disease-19
Subject Areas : Journal of Physical & Theoretical Chemistry
ghasem ghasemi
1
(Department of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran)
babak motahary
2
(Depatment of Computer Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran)
robabe Sayadikordabadi
3
(Department of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran)
Asghar Alizadehdakhel
4
(Department of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran)
Keywords: Covid-19, Autodock-vina, Molecular dynamics simulation, Molecular docking, Gromacs,
Abstract :
In this manuscript; Molecular dynamics simulation was tested on COVID -19 main protease (PDB: 6LU7) with the docking studies have been employed using autodock-vina-1.1.2-4 and autodock- mgltools-1.5.6 (flex) programs to evaluate the interactions. HIV-1 Protease is a prerequisite for viral replication. In this manuscript; Molecular dynamics simulation was tested on COVID -19 main protease (PDB: 6LU7) with the docking studies have been employed using autodock-vina-1.1.2-4 and autodock- mgltools-1.5.6 (flex) programs to evaluate the interactions. Regular and Flexible docking approaches were run. Molecular dynamics simulation was tested on COVID -19 main protease (PDB: 6LU7) with molecule 7. Drug-likeness descriptors of compounds such as logP (partition coefficient), H-Bond Acceptor (HBA), H-Bond Donor (HBD), number of Rotable Bond (nRB), and nHB calculated by DruLiTo. In the molecular docking study, the maximum binding affinity of -5.9 kcal/mol was obtained between each of COVID -19 main protease (PDB: 6LU7) enzyme systems and the geometric-optimized molecules, representing a strong interaction. The reference molecule PRD_002214 of Mpro forms four hydrogen bonds with Glu 166, Phe 140, Gln 189, His 163, and some hydrophobic bonds. In this study, molecules 7 (Amprenavir) and 15 were presented as the most stable ones that may be introduced for further investigations, including clinical experiments.