The physical properties and molecular structure of five natural indole alkaloids (IAs) and their interaction with protein targets have been studied, experimentally and theoretically. Electronic absorption (EAs) and CD spectroscopy, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), as well as imaging mass spectrometric techniques (IMS) were used, analyzing the isolated alkaloids and corresponding IAs/protein molecular complexes. Theoretical quantum chemical DFT calculations were also applied. The mechanism of their biological activity and structure-activity relationship as potential neurologically active compounds were studied, using the model interactions with 5HT2A receptors. The gas-phase stable molecular fragments of the IAs are discussed comparing the experimental mass spectrometric data and theoretical quantum chemical DFT calculations of the different molecular fragments of the IAs.
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