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Despite the intense development of vaccines and antiviral therapeutics, no specific treatment of coronavirus disease 2019 (COVID-19), caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently available Recently, X-ray crystallographic structures of a validated pharmacological target of SARS-CoV-2, the main protease (Mpro also called 3CLpro) in complex with peptide-like irreversible inhibitors have been published We have carried out computer-aided structure-based design and optimization of peptidomimetic irreversible α-ketoamide Mpro inhibitors and their analogues using MM, MD and QM/MM methodology, with the goal to propose lead compounds with improved binding affinity to SARS-CoV-2 Mpro, enhanced specificity for pathogenic coronaviruses, decreased peptidic character, and favourable drug-like properties The best inhibitor candidates designed in this work show largely improved interaction energies towards the Mpro and enhanced specificity due to 6 additional hydrogen bonds to the active site residues The presented results on new SARS-CoV-2 Mpro inhibitors are expected to stimulate further research towards the development of specific anti-COVID-19 drugs © 2020 The Royal Society of Chemistry
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