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Shuanghuanglian preparations and bioactive ingredients including baicalin and baicalein dose-dependently inhibited SARS-CoV-2 3CL protease and the replication of SARS-CoV-2 in cells. The crystal structure of SARS-CoV-2 3CL protease in complex with baicalein revealed a unique binding mode of this bioflavonoid as the first noncovalent, nonpeptidomimetic inhibitor of the protease.