Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (M <sup>pro</sup> ) through docking, molecular mechanic & dynamic, and ADMET profiling
Каріна Капуста, Supratik Kar, Jasmine T. Collins, Latasha M. Franklin, Wojciech Kołodziejczyk, Jerzy Leszczyński, Glake Hill
Abstract
proteins. To ensure the efficiency of the selected compounds, binding energies for top-15 hit ligands were calculated using Molecular Mechanics as well as their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were predicted. Based on predicted binding energies and toxicities, top-5 compounds were selected and subjected to Molecular Dynamics simulation and found to be stable in complex to act as possible inhibitors for SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
Topics & Concepts
Virtual screeningIn silicoDocking (animal)Protein Data Bank (RCSB PDB)Computational biologyDrug discoveryChemistrySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Protein Data BankMolecular dynamicsProteaseLipinski's rule of fiveDrugCoronavirus disease 2019 (COVID-19)Protein structurePharmacologyStereochemistryBiochemistryBiologyEnzymeComputational chemistryMedicineInfectious disease (medical specialty)DiseaseGeneNursingPathologyComputational Drug Discovery MethodsSynthesis and biological activitySARS-CoV-2 and COVID-19 Research