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• W3147172127 endingPage "2312" @default.
• W3147172127 startingPage "2302" @default.
• W3147172127 abstract "The COVID-19 pandemic has killed millions of people worldwide since its outbreak in December 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, developing an effective therapy is an urgent task, which requires accurately estimating the ligand-binding free energy to 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 the 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 molecular docking approach was manipulated using Autodock Vina (Vina) and Autodock4 (AD4) protocols to preliminarily investigate the ligand-binding affinity and pose to SARS-CoV-2 Mpro. The binding free energy was then refined using the fast pulling of ligand (FPL), linear interaction energy (LIE), molecular mechanics-Poisson-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 method, followed by LIE, FPL, and MM-PBSA (FEP > LIE ≈ FPL > MM-PBSA). Moreover, atomistic simulations revealed that the van der Waals interaction is the dominant factor. The residues Thr26, His41, Ser46, Asn142, Gly143, Cys145, His164, Glu166, and Gln189 are essential elements affecting the binding process. Our benchmark provides guidelines for further investigations using computational approaches." @default.
• W3147172127 created "2021-04-13" @default.
• W3147172127 creator A5010458646 @default.
• W3147172127 creator A5014938626 @default.
• W3147172127 creator A5077500815 @default.
• W3147172127 creator A5084131516 @default.
• W3147172127 date "2021-04-08" @default.
• W3147172127 modified "2023-10-11" @default.
• W3147172127 title "Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro" @default.
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• W3147172127 doi "https://doi.org/10.1021/acs.jcim.1c00159" @default.
• W3147172127 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8043216" @default.
• W3147172127 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33829781" @default.
• W3147172127 hasPublicationYear "2021" @default.
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