This research was based on virtual docking screening and molecular dynamics simulation among the 30 drugs analyzed, which drug had the best inhibitory effect on 3CL protease (Mpro) hydrolase. AutoDock Vina is used for molecular docking. Through our research, the binding affinity of saquinavir and raltegravir to the protein is higher than other candidate drugs in molecular docking; they are -9.1 kcal/mol and -9 kcal/mol, respectively. Among them remdesivir performance was mediocre, only -7.9 kcal/mol. In our study, ultimately, these systems are also basically stable. The overall contraction of the protein structure is most obvious after the combination of remdesivir. In the remdesivir-protein system, the structure of the terminal end has undergone relatively large changes. And the total number of hydrogen bonds formed in the remdesivir-protein system is larger. The hydrogen bonds can be maintained for a longer time, and the final interaction energy is stronger than other systems. These amino acid sequence fragments have high affinity with the remdesivir molecule. Remdesivir can change the structure of the protein to make it stronger in binding with itself through the interaction with the protein. The simulation study of drug screening for new coronaviruses can provide further support for new coronavirus effective drugs and provide powerful support to defeat the virus.
A Study of Potential SARS-CoV-2 Antiviral Drugs and Preliminary Research of Their Molecular Mechanism, Based on Anti-SARS-CoV Drug Screening and Molecular Dynamics Simulation.