|
?:abstract
|
-
COVID-19 pandemic has killed millions of people worldwide since its outbreak in Dec 2019 The pandemic is caused by the SARS-CoV-2 virus whose main protease (Mpro) is a promising drug target since it plays a key role in viral proliferation and replication Currently, designing an effective therapy is an urgent task, which requires accurately estimating ligand-binding free energy to the SARS-CoV-2 Mpro However, it should be noted that the accuracy of a free energy method probably depends on the protein target A highly accurate approach for some targets may fail to produce a reasonable correlation with experiment when a novel enzyme is considered as a drug target Therefore, in this context, the ligand-binding affinity to SARS-CoV-2 Mpro was calculated via various approaches The Autodock Vina (Vina) and Autodock4 (AD4) packages were manipulated to preliminary investigate the ligand-binding affinity and pose to the SARS-CoV-2 Mpro The binding free energy was then refined using the fast pulling of ligand (FPL), linear interaction energy (LIE), molecular mechanics-Poission Boltzmann surface area (MM-PBSA), and free energy perturbation (FEP) methods The benchmark results indicated that for docking calculations, Vina is more accurate than AD4 and for free energy methods, FEP is the most accurate followed by LIE, FPL and MM-PBSA (FEP > LIE > FPL >
|
![[This page as RDF]](https://research.tib.eu/covid-19/static/rdf-icon.gif){kind=icon}