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 F NMR spectroscopy and chemical fragment microarrays. Hit validation by SPR and H- 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.

Development of c-type lectin oriented surfaces for high avidity glycoconjugates: towards mimicking multivalent interactions on the cell surface

“…(2)(3)(4) These findings have placed DC-SIGN as an important therapeutic target and many efforts are being invested to develop DC-SIGN antagonists. (5)(6)(7)(8)(9)(10)(11)(12)(13) DC-SIGN is a tetrameric C-type lectin receptor (CLR) with specificity to D-mannose-and L-fucose-containing oligosaccharides that bind the C-terminal carbohydrate recognition domain (CRD) in a Ca2+-dependent manner. (1,14) Although the intrinsic affinity of a single CRD for a monosaccharide is low (KD in mM range), the global DC-SIGN/multivalent carbohydrates interaction affinity is markedly amplified (KD from µM to pM) through the avidity phenomenon.…”

Design and synthesis of glycomimetics: Recent advances

“…Modulation and control of the proteins involved is attracting increasing attention in the medicinal chemistry world. Only very recently, the identification of multiple secondary sites on lectins that can be targeted with drug‐like small molecules/fragments has been reported . In the case study reported by Aretz et al, the small molecules discovered do not bind to the sugar site in the CRD, but to a vicinal site that apparently allosterically controls the glycan binding site.…”

“…Only very recently, the identification of multiple secondary sites on lectins that can be targeted with drug‐like small molecules/fragments has been reported . In the case study reported by Aretz et al, the small molecules discovered do not bind to the sugar site in the CRD, but to a vicinal site that apparently allosterically controls the glycan binding site. The consequences of this novel binding mode to the downstream signaling events controlled by the glycan‐lectin interaction are so‐far unknown.…”

Selection of galectin‐3 ligands derived from genetically encoded glycopeptide libraries

“…Shallow topology of ligand‐binding sites in these proteins makes them a challenging target for high‐throughput screens and virtual screening/docking approaches . The presence of multiple binding sites, many of which do not coincide with a native carbohydrate recognition domain (CRD), poses an additional challenge for application of general ligand selection strategies to identify ligands for GBP . The ligands emanating from such screens often do not bind to CRD sites .…”

“…The presence of multiple binding sites, many of which do not coincide with a native carbohydrate recognition domain (CRD), poses an additional challenge for application of general ligand selection strategies to identify ligands for GBP . The ligands emanating from such screens often do not bind to CRD sites . Fragment‐based discovery could overcome the aforementioned problem by employing fragments that are known to bind to CRD.…”