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Isatin-based spiro indolenine alkaloids are derived from mixed biosynthetic origins, and the C-2 and C-3 carbonyl groups of isatin could be spirocyclic, thus achieving a variable chemical diversity. Four novel alkaloids (1a/1b, 2, and 3), featuring an unusual isatin-based spiro indolenine system, were obtained from the leaves of
Isatis indigotica
Fortune. Compounds 1a/1b were a pair of enantiomers characterized by an unprecedented 6/5/6/5/6 N,O-heterocyclic scaffold with a unique spiro[4.5] core. Compound 2 was the first 6/5/6/5/5/6 hexacyclic skeleton fused with an unexpected dispiro[4.4.0.4] system of an isatin-based alkaloid. Their structures were elucidated by 1D and 2D NMR and HRESIMS techniques as well as density functional theory (DFT) calculations and computer-assisted structure elucidation (CASE). The possible biosynthetic pathways for compounds 1a/1b–3 are proposed. In addition, all alkaloids were evaluated for their anti-neuroinflammatory and acetylcholinesterase inhibitory effects.