Programme

P.30 -- Poster, VCTP-46

Date: Tuesday, 5 October 2021

Time: 08:30 - 10:00

Study of SARS-CoV-2 main protease – X77 interaction at molecular scale using Molecular Dynamics Simulation

Tran Ba Duong (1), Lai Thi Thu Hien (1), Nguyen The Toan (1)

(1) Key Laboratory for Multiscale simulation of Complex Systems, Faculty of Physics,VNU University of Science, Vietnam National University

Global health is under heavy threat by a worldwide pandemic caused by SARS-CoV-2 virus (COVID-19). This pandemic was firstly detected at the end of December 2019 at the Wuhan seafood market in China, and quickly spread around the world. According to World Health Organization (WHO), there have been more than 190 million confirmed cases of COVID–19, including more than 4 million deaths all over the world. It has urgently imposed a great concern on the scientific community to find effective solutions to treat this virus. Although the most believed effective solution is vaccine, drug development against COVID-19 has also been necessary. More specifically, drugs are designed to inhibit target 3C-like protease (also called main protease or Mpro), which is responsible for the polyprotein cleavage. One ofthe potential ligands found in experiment, X77, was able to bind on pocket of Mpro with high affinity,reducing the virus’s ability to replicate. However, experimental results have not shown interactions that play a major role in the Mpro- X77 complex at the molecular scale in the physiological environmental condition. Therefore, we investigated the complex Mpro-X77 with three independent replicas of Molecular Dynamic Simulations, then calculate their binding energy using MM/PBSA method. Our results show that the whole protein SARS-CoV-2 Mpro and the X77 ligand are stable. In addition, the X77 ligand hashigh binding energy to this receptor with interactions to important residues THR25, LEU27, MET49,ASN142, CYS145, MET165, PRO168, HIS172, ASP187 and GLN189 that all in the catalytic pocket of the SARS-CoV-2 Mpro structure. These results lead to conclusion that X77 ligand is an effective inhibitor and could be used as a standard reference for the vitural screening and development of drugs for prevention and treatment of diseases caused by the SARS-CoV-2 virus.

Presenter: Tran Ba Duong