Initial study on SARS-CoV-2 main protease inhibition mechanism of some potential drugs using molecular docking simulation

Pham Minh Quan; Le Thi Thuy Huong; Tran Quoc Toan; Ngo Son Tung; Nguyen Trong Dan; Tran Thi Thu Thuy; Nguyen Manh Cuong; Pham Quoc Long

doi:10.15625/2525-2518/58/5/14914

Author affiliations

Authors

Pham Minh Quan Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam https://orcid.org/0000-0001-6922-1627
Le Thi Thuy Huong Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam
Tran Quoc Toan Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam
Ngo Son Tung Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
Nguyen Trong Dan Vietnam-Russia Tropical Center, Nguyen Van Huyen, Cau Giay, Hanoi, Viet Nam
Tran Thi Thu Thuy Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam
Nguyen Manh Cuong Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam
Pham Quoc Long Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Ha Noi, Viet Nam

DOI:

https://doi.org/10.15625/2525-2518/58/5/14914

Keywords:

COVID-19, SARS-CoV-2, autodock4, protease inhibitor, molecular docking

Abstract

The infection by the new coronavirus SARS-CoV-2 (called as COVID-19 disease) is a worldwide emergency, however, there is no antiviral treatment or vaccine until now. The crystal structure of SARS-CoV-2 main protease has been made publicity in the Protein Data Bank recently. Many efforts have been conducted by scientists including the use of several commercial medicines, however, understanding at atomic level how these compounds prevent SARS-CoV-2 protease is still lacking. In this context docking protocol was employed to rapidly estimate the binding affinity and binding pose of six drugs on the main protease.

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