Molecular Docking Study of Praeruptorin A-H and Qianhucoumarin A-J Binding to Divalent Metal Transporter-1 (DMT1)

The divalent metal transporter DMT1 (SLC11A2) is implicated in diverse human pathologies including cancers, inflammatory and degenerative diseases. Small molecules targeting this membrane protein are actively searched. Following the identification of the pyranocoumarin praeruptorin A as an inhibitor of ferroptosis that is able to bind to DMT1, we have investigated the interaction of related natural products with DMT1 using molecular modeling to determine structure-binding relationships. Two series of compounds were tested: praeruptorins A-H and qianhucoumarins A-J, all isolated previously from the roots of the Chinese medicinal plant Peucedanum praeruptorum Dunn (Bai-Hua Qian-Hu). The antitumor compound praeruptorin C was identified as the best DMT1 ligand in the series, with a binding capacity largely superior to that of praeruptorin A and also well superior to the reference organoselenium product ebselen, at least from an in silico perspective. Praeruptorin C, and to a lower extent praeruptorins F and H, can form stable complexes with DMT1 upon binding close to the ebselen binding site. Qianhucoumarins C and I were also identified as potential binders. Altogether, the analysis of the 18 natural products enabled identification of structural elements implicated in the target binding process. The curvature of the tricyclic pyranocoumarin scaffold and the angeloyl side chain at position 9 seem to contribute importantly to the protein interaction. An experimental validation is required but the docking study paves the way to the discovery and design of tricyclic coumarin derivatives targeting DMT1.