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Trehalose conjugates of 3-hydroxychromone (3HC) dyes have previously been utilized as fluorescence labels to detect metabolically active mycobacteria with a view to facilitating point-of-care detection of mycobacterial pathogens, especially <i>Mycobacterium tuberculosis</i>. We subjected the 3HC dye 2-(6-(diethylamino)benzofuran-2-yl)-3-hydroxy-4<i>H</i>-chromen-4-one (<b>3HC-2</b>) to a combined X-ray crystallography and density functional theory (DFT) study, and conducted preliminary fluorescence labelling experiments with the model organism <i>Mycobacterium aurum</i>. In the crystal, <b>3HC-2</b> exhibits an s-<i>cis</i> conformation of the chromone and the benzofuran moieties about the central C–C bond. According to DFT calculations, the <i>s</i>-<i>cis</i> conformer is about 1.8 kcal mol⁻¹ lower in energy than the <i>s</i>-<i>trans</i> conformer. The solid-state supramolecular structure features hydrogen-bonded dimers and π…π stacking. Fluorescence microscopy revealed fluorescence of <i>M. aurum</i> cells treated with the dye trehalose conjugate <b>3HC-2-Tre</b> in the GFP channel. It was concluded that s-<i>cis</i> is the preferred conformation of <b>3HC-2</b> and that the generally considered non-pathogenic <i>M. aurum</i> can be labelled with the fluorescence probe <b>3HC-2-Tre</b> for convenient in vitro drug screening of new antimycobacterial agents.