Identification of Multiple Druggable Secondary Sites by Fragment Screening against DC-SIGN

Abstract

DC-SIGN is a cell-surface receptor for several pathogenic threats, such as HIV, Ebola virus, or Mycobacterium tuberculosis. Multiple attempts to develop inhibitors of the underlying carbohydrate-protein interactions have been undertaken in the past fifteen years. Still, drug-like DC-SIGN ligands are sparse, which is most likely due to its hydrophilic, solvent-exposed carbohydrate-binding site. Herein, we report on a parallel fragment screening against DC-SIGN applying SPR and a reporter displacement assay, which complements previous screenings using ¹⁹ F NMR spectroscopy and chemical fragment microarrays. Hit validation by SPR and ¹ H-¹⁵ N HSQC NMR spectroscopy revealed that although no fragment bound in the primary carbohydrate site, five secondary sites are available to harbor drug-like molecules. Building on key interactions of the reported fragment hits, these pockets will be targeted in future approaches to accelerate the development of DC-SIGN inhibitors.

Keywords: NMR spectroscopy; drug discovery; fragment-based drug design; glycan-binding proteins; surface plasmon resonance.