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The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described. Here, we report the structure-based development of several chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution X-ray protein crystallography, and binding evaluation with in-solution assays. Potent scaffolds were designed with in silico linkage of previously obtained fragment hits and ultra-large library docking screens of more than 450 million molecules. In total, 160 hits comprising 119 different scaffolds were discovered and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Ã… resolution or better. The structure-activity-relationships emerging from this study may template future drug development against Mac1. Summary: Computational fragment-linking and ultra-large library docking identifies potent inhibitors of the SARS-CoV-2 macrodomain.

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