Synthesis and structure-activity relationship studies of thiazole derivatives as inhibitors of SARS-CoV-2 main protease

Abstract

Among the various potential drug targets in SARS-CoV-2, the main protease has emerged as a viable target for antiviral drug development. In this project, 42 thiazole and oxazole derivatives were designed and synthesized through a structure-based rational drug design approach. Biochemical screening and IC50 assessments indicated that 5-chloropyridin-3-yl 2-(methyl(phenyl)amino)thiazole-4-carboxylate (compound MC12) is a potent SARS-CoV-2 Mpro inhibitor, with efficacy comparable to Nirmatrelvir. Compound MC12 also displayed the inhibitory activity against SARS-CoV Mpro. The structure-activity relationship of these compounds was further explored. The mechanism of inhibition was elucidated by mass spectrometry and X-ray crystal structure as covalent bond formation between the inhibitor and target. The compounds showed minimal cytotoxicity in MTT assays on mammalian cell lines and demonstrated antiviral activity against SARS-CoV-2 in Vero E6 cells. Structural modifications of MC12, such as the derivative 5-chloropyridin-3-yl 2-(((1H-benzo[d][1,2,3]triazol-1-yI)methyl)(benzyl)-amino)thiazole-4-carboxylate (compound MC04BP01), were also explored. MC04BP01 exhibits inhibitory activity against SARS-CoV-2 Mpro similar to that used for MC12 and Nirmatrelvir. 2-Chloro-N-((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopyrro-lidin-3-yl)propan-2-yl)amino)pentan-2-yl)thiazole-4-carboxamide (compound AD05) and 2-chloro-N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxo-pyrrolidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)thiazole-4-carboxamide (compound AD06), belonging to peptidomimetic derived from MC compounds, demonstrate inhibitory effects against the main protease. AD06 demonstrated an IC50 value against SARS-CoV-2 Mpro that was similar to that of Nirmatrelvir. Furthermore, the analysis of X-ray crystal structures of SARS-CoV-2 Mpro in complex with AD05 and AD06 confirmed the covalent binding mechanism of the AD series of compounds. The antiviral assay results indicated that AD05 displayed the strongest potency (EC50 = 3.264 μM) against the SARS-CoV-2 virus. These findings highlight the potential of thiazole-based compounds as promising leads in the development of SARS-CoV-2 Mpro inhibitors.